Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

A - Variable in class etomica.conjugategradient.ConjugateGradients
A - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
A - Variable in class etomica.conjugategradient.SteepestDescent
a - Variable in class etomica.dimer.P1LepsHarmonic
A - Variable in class etomica.meam.ParameterSetMEAM
a - Variable in class etomica.meam.ParameterSetMEAM
A - Variable in class etomica.meam.PotentialCuLREP
A - Variable in class etomica.meam.PotentialEFS
a - Variable in class etomica.meam.PotentialFeEAM
A - Variable in class etomica.models.co2.P2CO2Hellmann
a - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
a - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
a - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
a - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
a - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
a - Variable in class etomica.models.water.P2Water4PSoft
A - Variable in class etomica.models.water.PNWaterGCPM
A(double) - Method in class etomica.modules.adsorption.EOSSWPatel
a - Variable in class etomica.modules.rheology.IntegratorPolymer
a - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
A - Variable in class etomica.potential.P2HePCKLJS
a - Static variable in class etomica.potential.P2HePCKLJS
a - Variable in class etomica.potential.P2HSDipole
a - Variable in class etomica.potential.P2LJDipole
A - Variable in class etomica.potential.P2NitrogenHellmann
a - Variable in class etomica.potential.P2ReactionFieldDipole
A - Variable in class etomica.potential.P3CPSNonAdditiveHe
A - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
A - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
A - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
A - Variable in class etomica.potential.P3HydrogenManzhos
a - Variable in class etomica.potential.PotentialCalculationPhiSum
a - Static variable in class etomica.statmech.HardSphereFluid
a - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
a - Variable in class etomica.util.numerical.NonLinearCurveFitting
a - Variable in class etomica.util.numerical.PadeApproximation
a - Static variable in class etomica.veos.bigdecimal.Euler
a - Static variable in class etomica.veos.bigdecimal.PartitionsP: The list of all partitions as a vector.
a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
a - Variable in class etomica.virial.MCMoveClusterAtomHSTree
a - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
a0 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
a0 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
a0 - Variable in class etomica.meam.PotentialFeEAM_LS
a0 - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
a0 - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
A0 - Variable in class etomica.potential.P2HeSimplified
a0 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
a0 - Variable in class etomica.potential.P4BondTorsion
a0 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
a0 - Variable in class etomica.potential.Potential2SoftSphericalLS
A0 - Static variable in class etomica.statmech.HardSphereSolid
A1 - Variable in class etomica.dimer.P1LepsHarmonic
A1 - Variable in class etomica.models.nitrogen.P2Nitrogen
A1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
A1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
A1(double) - Method in class etomica.modules.adsorption.EOSSWPatel
A1 - Variable in class etomica.potential.P2HeSimplified
a1 - Variable in class etomica.potential.P2QChemInterpolated
a1 - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
a1 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
a1 - Variable in class etomica.potential.P3QChem.DampingParams
a1 - Variable in class etomica.potential.P4BondTorsion
a1 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
a1 - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
A2 - Variable in class etomica.dimer.P1LepsHarmonic
A2 - Variable in class etomica.models.nitrogen.P2Nitrogen
A2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
A2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
A2 - Variable in class etomica.potential.P2HeSimplified
a2 - Variable in class etomica.potential.P2QChemInterpolated
a2 - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
a2 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
a2 - Variable in class etomica.potential.P3QChem.DampingParams
a2 - Variable in class etomica.potential.P4BondTorsion
a2 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
a2 - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
A3 - Variable in class etomica.potential.P2HeSimplified
a3 - Variable in class etomica.potential.P4BondTorsion
a3 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
AA - Static variable in class etomica.models.co2.P2CO2Hellmann
AA - Static variable in class etomica.potential.P2NitrogenHellmann
AAbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
AAlphaFunction(int, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
aam - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
aamOriented - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
AandPAlpha(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
AandPBeta(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal
ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
AB - Static variable in class etomica.models.co2.P2CO2Hellmann
AB - Static variable in class etomica.potential.P2NitrogenHellmann
ABbonded - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
ABbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
ABetaFunction(int, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
abicipeso4(double, double, double, double) - Static method in class etomica.potential.P2O2Bartolomei
AbnormalCompletionException - Exception in etomica.exception: Exception that indicates a method is defined for a class (perhaps to adhere to an interface), but its implementation is not yet completed.
AbnormalCompletionException() - Constructor for exception etomica.exception.AbnormalCompletionException: Constructor for AbnormalCompletionException
AbnormalCompletionException(String) - Constructor for exception etomica.exception.AbnormalCompletionException: Constructor for MethodNotImplementedException.
aBonds - Variable in class etomica.virial.cluster.VirialDiagramsPT
AboutBoxWindow - Class in etomica.graphics
AboutBoxWindow(Component, String) - Constructor for class etomica.graphics.AboutBoxWindow
AboutBoxWindow(Component) - Constructor for class etomica.graphics.AboutBoxWindow
AboutBoxWindow(Component, String, String[], String[]) - Constructor for class etomica.graphics.AboutBoxWindow
AboutBoxWindow.EtomicaGraphic - Class in etomica.graphics
abParams - Variable in class etomica.graph.operations.MaxIsomorphWertheim.MaxIsomorphWertheimParameters
Abs() - Constructor for class etomica.util.Function.Abs
abs() - Method in class etomica.veos.bigdecimal.BigSurd: Absolute value.
abs() - Method in class etomica.veos.bigdecimal.Rational: Absolute value.
AbstractBitmap - Class in etomica.graph.model.impl
AbstractBitmap() - Constructor for class etomica.graph.model.impl.AbstractBitmap
AbstractLattice - Interface in etomica.lattice: Interface for a generic lattice, which is a collection of sites that can be accessed individually via specification of a set of integers.
AbstractOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.AbstractOptionHandler
AbstractSearchState - Class in etomica.graph.isomorphism
AbstractSearchState() - Constructor for class etomica.graph.isomorphism.AbstractSearchState
AbstractSearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.AbstractSearchState
AbstractTraversal - Class in etomica.graph.traversal
AbstractTraversal() - Constructor for class etomica.graph.traversal.AbstractTraversal
ac - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
ac - Variable in class etomica.modules.multiharmonic.DataProcessorVar
acc - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
acc - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
accept(IAtom) - Method in interface etomica.atom.AtomFilter: Returns true if atom is passes test of filter.
accept(IMolecule) - Method in interface etomica.atom.AtomFilter
accept(IAtom) - Method in class etomica.atom.AtomFilterInShape: Returns true if the atom's position is inside the shape.
accept(IMolecule) - Method in class etomica.atom.AtomFilterInShape
accept(IAtom) - Method in class etomica.atom.AtomFilterStatic
accept(IMolecule) - Method in class etomica.atom.AtomFilterStatic
accept(Graph) - Method in class etomica.graph.iterators.filters.FieldNodeCount
accept(Graph, Set<Graph>) - Method in class etomica.graph.iterators.filters.GlobalFilter
accept(Graph, Set<Graph>) - Method in class etomica.graph.iterators.filters.IdenticalGraphFilter
accept(Graph, Set<Graph>) - Method in class etomica.graph.iterators.filters.IsomorphismFilter
accept(Graph) - Method in class etomica.graph.iterators.filters.LocalFilter
accept(Graph) - Method in class etomica.graph.iterators.filters.PropertyFilter
accept(File) - Method in class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
accept(IAtom) - Method in class etomica.lattice.LatticePlane
accept(IMolecule) - Method in class etomica.lattice.LatticePlane
accept(IAtom) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
accept(IMolecule) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
accept(IAtomList) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
accept(IAtom) - Method in class etomica.modules.droplet.AtomFilterLiquid
accept(IMolecule) - Method in class etomica.modules.droplet.AtomFilterLiquid
accept(IAtom) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
accept(IMolecule) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
accept(IAtomList) - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder.AtomFilterInCylinder
accept(IAtomList) - Method in class etomica.modules.render.RenderMD.CriterionCar
accept(IAtomList) - Method in class etomica.modules.sam.CriterionTether3
accept(IAtomList) - Method in class etomica.nbr.CriterionAdapter: Implementation of this method should introduce new criterion and return true if pair meets this criterion and that of the wrapped NeighborCriterion.
accept(IAtomList) - Method in class etomica.nbr.CriterionAll: Always returns true, indicating that all atoms pairs are neighbors.
accept(IAtomList) - Method in class etomica.nbr.CriterionBondedSimple
accept(IAtomList) - Method in class etomica.nbr.CriterionInterMolecular
accept(IAtomList) - Method in class etomica.nbr.CriterionMolecular: Returns false if pair is/isn't in same molecule (depending on setting of intraMolecular); if matches this criterion, return value will be that given by any subCriterion.
accept(IAtomList) - Method in class etomica.nbr.CriterionMolecularNonAdjacent
accept(IAtomList) - Method in class etomica.nbr.CriterionNone: Always returns false, indicating that no atoms pairs are neighbors.
accept(IAtomList) - Method in class etomica.nbr.CriterionPositionWall
accept(IAtomList) - Method in class etomica.nbr.CriterionSimple
accept(IAtomList) - Method in class etomica.nbr.CriterionType: Returns true if the AtomType of the atom matches the AtomType given at construction and if the wrapped criterion accept also returns true.
accept(IAtomList) - Method in class etomica.nbr.CriterionTypePair: Returns true if the AtomTypes for the pair of atoms match the AtomTypes given at construction (without regard to the order of the pair), and if the wrapped criterion also accepts the pair.
accept(IAtomList) - Method in class etomica.nbr.CriterionTypesCombination: Returns true if the AtomTypes for the pair of atoms match the AtomTypes given at construction (without regard to the order of the AtomSet), and if the wrapped criterion also accepts the AtomSet.
accept(IAtomList) - Method in class etomica.nbr.CriterionTypesMulti: Returns true if the AtomTypes for the pair of atoms match the AtomTypes given at construction (without regard to the order of the AtomSet), and if the wrapped criterion also accepts the AtomSet.
accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular: Implementation of this method should introduce new criterion and return true if pair meets this criterion and that of the wrapped NeighborCriterion.
accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionAllMolecular: Always returns true, indicating that all atoms pairs are neighbors.
accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSpecies: Returns true if the species of the molecule matches the Species given at construction and if the wrapped criterion accept also returns true.
accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSpeciesPair: Returns true if the Species for the pair of molecules match the Species given at construction (without regard to the order of the pair), and if the wrapped criterion also accepts the pair.
accept(IMoleculeList) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
accept(IAtomList) - Method in interface etomica.nbr.NeighborCriterion
ACCEPT_ALL - Static variable in class etomica.atom.AtomFilterStatic: Static instance of a filter that accepts all atoms.
ACCEPT_NONE - Static variable in class etomica.atom.AtomFilterStatic: Static instance of a filter that rejects all atoms.
acceptanceProbability() - Method in class etomica.integrator.mcmove.MCMoveTracker: Returns the average probability of accepting the move associated with this tracker.
acceptanceRatio() - Method in class etomica.integrator.mcmove.MCMoveTracker: Returns the fraction of accepted trials of the move associated with this tracker.
acceptanceTarget - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
acceptNotify() - Method in class etomica.association.MCMoveBiasUB
acceptNotify() - Method in class etomica.association.MCMoveBiasUBMolecule
acceptNotify() - Method in class etomica.association.MCMoveDimer: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.association.MCMoveDimerRotate: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.association.MCMoveSmer: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.association.MCMoveSmerRotate: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.association.MCMoveVolumeAssociated
acceptNotify() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
acceptNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
acceptNotify() - Method in class etomica.integrator.mcmove.MCMove: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveAtom: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveDimer: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveMolecule: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration: Swaps positions of molecules in two boxes.
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveVolume
acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
acceptNotify() - Method in class etomica.models.hexane.MCMoveCBMC
acceptNotify() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
acceptNotify() - Method in class etomica.models.hexane.MCMoveReptate
acceptNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
acceptNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
acceptNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
acceptNotify() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
acceptNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
acceptNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
acceptNotify() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
acceptNotify() - Method in class etomica.modules.adsorption.MyMCMove
acceptNotify() - Method in class etomica.modules.dcvgcmd.MyMCMove
acceptNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupled: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveAtomSuperBox: Method called by IntegratorMC in the event that the most recent trial is accepted.
acceptNotify() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
acceptNotify() - Method in class etomica.normalmode.MCMoveHarmonic
acceptNotify() - Method in class etomica.normalmode.MCMoveHarmonicStep
acceptNotify() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
acceptNotify() - Method in class etomica.normalmode.MCMovePhaseAngle
acceptNotify() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
acceptNotify() - Method in class etomica.normalmode.MCMoveSingleMode
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolid
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
acceptNotify() - Method in class etomica.normalmode.MCMoveWV
acceptNotify() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
acceptNotify() - Method in class etomica.spin.MCMoveSpinFlip
acceptNotify() - Method in class etomica.virial.BoxCluster: Informs the box that the trial was accepted so it will keep the new coordinate pairs.
acceptNotify() - Method in class etomica.virial.MCMoveChangeBondLength
acceptNotify() - Method in class etomica.virial.MCMoveClusterAngleBend
acceptNotify() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtom
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSChain
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSRing
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSTree
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomMulti
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomQ
acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
acceptNotify() - Method in class etomica.virial.MCMoveClusterDiagram
acceptNotify() - Method in class etomica.virial.MCMoveClusterMolecule
acceptNotify() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
acceptNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
acceptNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
acceptNotify() - Method in class etomica.virial.MCMoveClusterReptateMulti
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrow
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
acceptNotify() - Method in class etomica.virial.MCMoveClusterRingScale
acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateCH3
acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionMulti
acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleMulti
acceptNotify() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster: Swaps positions of molecules in two boxes.
accRefUa2 - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
accTargetUa2 - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
accumulator - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
accumulator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
accumulator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
accumulator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
accumulator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
accumulator - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
accumulator - Variable in class etomica.virial.simulations.SimulationVirial
accumulator - Variable in class etomica.virial.simulations.SimulationVirialPT
accumulator1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
accumulator2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
accumulatorAction - Variable in class etomica.action.SimulationRestart
AccumulatorAverage - Class in etomica.data: Accumulator that keeps statistics for averaging and error analysis.
AccumulatorAverage() - Constructor for class etomica.data.AccumulatorAverage: Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverage(long) - Constructor for class etomica.data.AccumulatorAverage
accumulatorAverage - Variable in class etomica.graphics.DisplayTextBoxesCAE
AccumulatorAverage.StatType - Class in etomica.data: Enumerated type that can be used to indicated the statistic to be taken from the accumulator (e.g., average, error, current value, etc.).
AccumulatorAverageBlockless - Class in etomica.data: AccumulatorAverage that does not use blocks (best used when each sample is independent).
AccumulatorAverageBlockless() - Constructor for class etomica.data.AccumulatorAverageBlockless: Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageBlockless.AllData - Class in etomica.data
AccumulatorAverageBlockless.StatType - Class in etomica.data: Enumerated type that can be used to indicated the statistic to be taken from the accumulator (e.g., average, error, current value, etc.).
AccumulatorAverageBlocklessSlim - Class in etomica.data: AccumulatorAverage that does not use blocks (best used when each sample is independent).
AccumulatorAverageBlocklessSlim() - Constructor for class etomica.data.AccumulatorAverageBlocklessSlim
AccumulatorAverageBlocklessSlim.StatType - Class in etomica.data: Enumerated type that can be used to indicated the statistic to be taken from the accumulator (e.g., average, error, current value, etc.).
AccumulatorAverageCollapsing - Class in etomica.data: AccumulatorAverage that adjusts the block size during the simulation.
AccumulatorAverageCollapsing() - Constructor for class etomica.data.AccumulatorAverageCollapsing: Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageCollapsing(int) - Constructor for class etomica.data.AccumulatorAverageCollapsing
AccumulatorAverageCollapsing(int, int) - Constructor for class etomica.data.AccumulatorAverageCollapsing
AccumulatorAverageCollapsingLog - Class in etomica.data: AccumulatorAverage that keeps track of block averages and standard deviations corresponding to all block sizes from 1 to the n where n is the largest power of 2 less than the current number of samples.
AccumulatorAverageCollapsingLog() - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
AccumulatorAverageCollapsingLog(int) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog: With this constructor, the accumulator will use an internal RNG with a set seed such that each resampling of the data will be identical (the same set of samples will go into the averages and the standard deviations, etc).
AccumulatorAverageCollapsingLog(IRandom) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
AccumulatorAverageCollapsingLog(IRandom, int) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
AccumulatorAverageCollapsingLogAB - Class in etomica.data
AccumulatorAverageCollapsingLogAB() - Constructor for class etomica.data.AccumulatorAverageCollapsingLogAB
AccumulatorAverageCollapsingLogAB(IRandom) - Constructor for class etomica.data.AccumulatorAverageCollapsingLogAB
AccumulatorAverageCovariance - Class in etomica.data: Class that does the work of AccumulatorAverageFixed and also calculates the covariance of the incoming data values (the covariance of each value with each other value, as well as itself (which is actually its standard deviation)) as well as the covariance of the block averages of the different data quantities.
AccumulatorAverageCovariance() - Constructor for class etomica.data.AccumulatorAverageCovariance
AccumulatorAverageCovariance(boolean) - Constructor for class etomica.data.AccumulatorAverageCovariance
AccumulatorAverageCovariance(long) - Constructor for class etomica.data.AccumulatorAverageCovariance
AccumulatorAverageCovariance(long, boolean) - Constructor for class etomica.data.AccumulatorAverageCovariance
AccumulatorAverageFixed - Class in etomica.data: AccumulatorAverage that maintains a fixed block size.
AccumulatorAverageFixed() - Constructor for class etomica.data.AccumulatorAverageFixed: Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageFixed(long) - Constructor for class etomica.data.AccumulatorAverageFixed
AccumulatorAverageFixedOutputFile - Class in etomica.data: AccumulatorAverage that maintains a fixed block size.
AccumulatorAverageFixedOutputFile() - Constructor for class etomica.data.AccumulatorAverageFixedOutputFile: Default constructor sets block size to Default value, and sets the interval for pushing the output data (pushInterval) to 100.
AccumulatorAverageFixedOutputFile(int) - Constructor for class etomica.data.AccumulatorAverageFixedOutputFile
AccumulatorCounter - Class in etomica.data: Data processor that simply counts the number of times its addData method is invoked.
AccumulatorCounter() - Constructor for class etomica.data.AccumulatorCounter
AccumulatorHistogram - Class in etomica.data: Accumulator that keeps histogram of data.
AccumulatorHistogram() - Constructor for class etomica.data.AccumulatorHistogram: Creates instance using HistogramSimple factory and specifying histograms having 100 bins.
AccumulatorHistogram(Histogram) - Constructor for class etomica.data.AccumulatorHistogram: Creates instance using given histogram factory with default nBins of 100.
AccumulatorHistogram(Histogram, int) - Constructor for class etomica.data.AccumulatorHistogram: Creates instance using the given histogram factory making histograms having the given number of bins.
AccumulatorHistory - Class in etomica.data: Accumulator that keeps history of data.
AccumulatorHistory() - Constructor for class etomica.data.AccumulatorHistory: Creates instance using HistorySimple factory and specifying historys having 100 bins.
AccumulatorHistory(History) - Constructor for class etomica.data.AccumulatorHistory
accumulatorHistory - Variable in class etomica.graphics.ActionHistoryWindow
AccumulatorHistory.DataSourceCount - Class in etomica.data: Simple DataSource to use as a default time DataSource.
AccumulatorOverlapAverageUa2 - Class in etomica.modules.multiharmonic.overlap: Accumulator for taking ratio between two sums (and pretend it's an "average") Data added to this accumulator must be a 2-element DataDoubleArray
AccumulatorOverlapAverageUa2(int, boolean) - Constructor for class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
accumulatorPE - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
accumulatorPump - Variable in class etomica.virial.simulations.SimulationVirial
accumulatorPump - Variable in class etomica.virial.simulations.SimulationVirialPT
accumulatorPumps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
accumulatorPumps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
accumulatorPumps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
accumulatorPumps - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImage
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
accumulatorPumps - Variable in class etomica.normalmode.SimOverlap
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapLJ
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapLJModule
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapModule
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphere
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSSnxy
accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialOverlap
accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
AccumulatorRatioAverage - Class in etomica.data: Accumulator for calculating ratio between two sums
AccumulatorRatioAverage() - Constructor for class etomica.data.AccumulatorRatioAverage
AccumulatorRatioAverage(long) - Constructor for class etomica.data.AccumulatorRatioAverage
AccumulatorRatioAverageCovariance - Class in etomica.data: Accumulator for calculating ratio between sums.
AccumulatorRatioAverageCovariance() - Constructor for class etomica.data.AccumulatorRatioAverageCovariance
AccumulatorRatioAverageCovariance(long) - Constructor for class etomica.data.AccumulatorRatioAverageCovariance
AccumulatorRatioAverageCovarianceFull - Class in etomica.data: Accumulator for calculating ratio between sums.
AccumulatorRatioAverageCovarianceFull() - Constructor for class etomica.data.AccumulatorRatioAverageCovarianceFull
AccumulatorRatioAverageCovarianceFull(long) - Constructor for class etomica.data.AccumulatorRatioAverageCovarianceFull
accumulators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
accumulators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
accumulators - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
accumulators - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImage
accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
accumulators - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
accumulators - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
accumulators - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
accumulators - Variable in class etomica.normalmode.SimOverlap
accumulators - Variable in class etomica.normalmode.SimOverlapLJ
accumulators - Variable in class etomica.normalmode.SimOverlapLJModule
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphere
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
accumulators - Variable in class etomica.normalmode.SimOverlapSSnxy
accumulators - Variable in class etomica.virial.MeterVirialBDBin
accumulators - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
accumulators - Variable in class etomica.virial.simulations.SimulationVirialOverlap
accumulators - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
AccumulatorVirialOverlapSingleAverage - Class in etomica.virial.overlap: Accumulator for taking ratio between two sums (and pretend it's an "average") Data added to this accumulator must be a 2-element DataDoubleArray
AccumulatorVirialOverlapSingleAverage(int, boolean) - Constructor for class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
AccumulatorVirialOverlapSingleAverage(long, int, boolean) - Constructor for class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
AceticAcidMCParam() - Constructor for class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
AceticAcidModPotentialHelper - Class in etomica.models.OPLS: PotentialHelper class of acetic acid using improved OPLS (or TraPPE) united atom model
AceticAcidModPotentialHelper() - Constructor for class etomica.models.OPLS.AceticAcidModPotentialHelper
AceticAcidPotentialHelper - Class in etomica.models.OPLS: PotentialHelper class of acetic acid using OPLS united atom model
AceticAcidPotentialHelper() - Constructor for class etomica.models.OPLS.AceticAcidPotentialHelper
ACollectionBondedPotential - Class in etomica.virial.GUI.components
ACollectionBondedPotential() - Constructor for class etomica.virial.GUI.components.ACollectionBondedPotential
acos(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The inverse trigonometric cosine.
acosh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The inverse hyperbolic cosine.
action - Variable in class etomica.action.activity.ControllerEvent
action - Variable in class etomica.util.Grabber.CornerSetListener
ActionConfigWindow - Class in etomica.graphics: Action that opens a new window and dumps the coordinates into the window.
ActionConfigWindow(IBox) - Constructor for class etomica.graphics.ActionConfigWindow
ActionCornerSetter(Grabber, int) - Constructor for class etomica.util.Grabber.ActionCornerSetter
actionExceptionMap - Variable in class etomica.action.activity.Controller
ActionGraphic - Class in etomica.graphics: Wrapper of an etomica Action that permits it to be used as a java.awt action listener.
ActionGraphic(IAction) - Constructor for class etomica.graphics.ActionGraphic
ActionGroup - Interface in etomica.action
ActionGroupSeries - Class in etomica.action: A set of Action instances grouped and performed in series as if a single action.
ActionGroupSeries() - Constructor for class etomica.action.ActionGroupSeries: Constructs an action group that holds no actions.
ActionGroupSeries(IAction[]) - Constructor for class etomica.action.ActionGroupSeries: Defines group via the given array of actions.
actionHash - Variable in class etomica.graphics.DeviceSelector
ActionHistoryWindow - Class in etomica.graphics: Action that opens a new window and dumps the coordinates into the window.
ActionHistoryWindow(AccumulatorHistory) - Constructor for class etomica.graphics.ActionHistoryWindow
ActionIntegrate - Class in etomica.action: Action that repeatedly invokes an Integrator's doStep method.
ActionIntegrate(IIntegrator) - Constructor for class etomica.action.ActionIntegrate: Constructs activity to generate configurations with the given integrator.
ActionIntegrate(IIntegrator, boolean) - Constructor for class etomica.action.ActionIntegrate
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
actionIntegrator - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
actionIntegrator - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
actionIntegrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT
actionIntegrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
actionIntegrator - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
actionIntegrator - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
ActionMoveWall(DeviceSlider, Sam, IAction) - Constructor for class etomica.modules.sam.SamGraphic.ActionMoveWall
actionPerformed() - Method in class etomica.action.ActionGroupSeries: Invokes the actionPerformed method of all actions in the method, in the order given by the array at construction.
actionPerformed() - Method in class etomica.action.ActionIntegrate: Main loop for conduct of integration.
actionPerformed() - Method in class etomica.action.ActionToggle: Toggles the state of the target object (true to false, false to true).
actionPerformed() - Method in class etomica.action.Activity: Sets integrator to begin isActive on its own thread.
actionPerformed(IAtom) - Method in interface etomica.action.AtomAction
actionPerformed(IAtom) - Method in class etomica.action.AtomActionRandomizeVelocity: Assigns velocity to atom with components selected from a Maxwell-Boltzmann distribution with temperature most recently set for the action.
actionPerformed(IAtom) - Method in class etomica.action.AtomActionRotateBy
actionPerformed(IAtom) - Method in class etomica.action.AtomActionTranslateBy
actionPerformed() - Method in class etomica.action.BoxDeleteMolecules: Performs the action of deleting accept == false molecules, considering all molecules in the box last given to setBox.
actionPerformed() - Method in class etomica.action.BoxImposePbc
actionPerformed() - Method in class etomica.action.BoxInflate: Performs boundary dimension change
actionPerformed() - Method in class etomica.action.BoxInflateAnisotropic: Performs anisotropic inflation.
actionPerformed() - Method in class etomica.action.BoxInflateDeformable: Performs isotropic inflation.
actionPerformed() - Method in class etomica.action.BoxQuench
actionPerformed() - Method in class etomica.action.BoxRandomizeMomenta
actionPerformed() - Method in class etomica.action.BoxScaleMomenta
actionPerformed() - Method in class etomica.action.CalcVibrationalModes
actionPerformed() - Method in class etomica.action.ControllerToggle
actionPerformed() - Method in interface etomica.action.IAction: Completes the action defined by the class implementing this interface.
actionPerformed() - Method in class etomica.action.IntegratorReset
actionPerformed(IMolecule) - Method in interface etomica.action.MoleculeAction
actionPerformed(IMolecule) - Method in class etomica.action.MoleculeActionTranslateTo
actionPerformed(IMolecule) - Method in class etomica.action.MoleculeChildAtomAction
actionPerformed() - Method in class etomica.action.PDBWriter
actionPerformed() - Method in class etomica.action.SimulationDataAction
actionPerformed() - Method in class etomica.action.SimulationRestart: Resets boxs, integrators, and accumulators.
actionPerformed() - Method in class etomica.action.WriteConfiguration: Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() - Method in class etomica.action.WriteConfigurationBinary: Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() - Method in class etomica.action.WriteConfigurationDLPOLY: Writes the leaf Atom coordinates to the file confName.pos_new.
actionPerformed() - Method in class etomica.action.WriteConfigurationP2DLPOLY: Writes the leaf Atom coordinates to the file CONFIG.
actionPerformed() - Method in class etomica.action.XYZWriter
actionPerformed(IEvent) - Method in class etomica.association.AssociationManager
actionPerformed(IEvent) - Method in class etomica.association.AssociationManagerMolecule
actionPerformed(IEvent) - Method in class etomica.data.DataLogger: Close file when integrator is done.
actionPerformed() - Method in class etomica.data.DataPump: Transmits the data from the source to the sink.
actionPerformed() - Method in class etomica.data.DataPumpListenerPow
actionPerformed() - Method in class etomica.data.DataPumpListenerSmart
actionPerformed() - Method in class etomica.data.DataStreamAction
actionPerformed(Object) - Method in class etomica.data.DataStreamAction
actionPerformed() - Method in class etomica.data.meter.MeterDihedralAngle: Measures the dihedral angle's for the current configuration of the given box.
actionPerformed() - Method in class etomica.data.meter.MeterRDF: Takes the RDF for the current configuration of the given box.
actionPerformed() - Method in class etomica.data.meter.MeterRDFPC: Takes the RDF for the current configuration of the given box.
actionPerformed() - Method in class etomica.data.meter.MeterStructureFactor
actionPerformed() - Method in class etomica.graphics.ActionConfigWindow
actionPerformed(ActionEvent) - Method in class etomica.graphics.ActionGraphic
actionPerformed() - Method in class etomica.graphics.ActionGraphic
actionPerformed() - Method in class etomica.graphics.ActionHistoryWindow
actionPerformed() - Method in class etomica.graphics.ActionVelocityWindow
actionPerformed() - Method in class etomica.graphics.Device.ActionSet
actionPerformed(ActionEvent) - Method in class etomica.graphics.DisplayPlot.DataWriter
actionPerformed(ActionEvent) - Method in class etomica.graphics.DisplayPlot.RawDataWindowOpener
actionPerformed() - Method in class etomica.graphics.DisplayPolytope
actionPerformed(IEvent) - Method in class etomica.integrator.IntegratorPT.BoxTracker: Method called when two boxes are successfully exchanged.
actionPerformed() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
actionPerformed() - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
actionPerformed() - Method in class etomica.mappedvirial.MeterMeanForce
actionPerformed() - Method in class etomica.models.hexane.CheckCBMCHexane
actionPerformed() - Method in class etomica.models.hexane.ShowStep
actionPerformed(IAtom) - Method in class etomica.models.nitrogen.AtomActionTransformed
actionPerformed() - Method in class etomica.models.nitrogen.MeterNormalizedCoord: Assigning the histogram to data
actionPerformed() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta: Assigning the histogram to data
actionPerformed() - Method in class etomica.models.nitrogen.MeterOrientationDistribution: Assigning the histogram to data
actionPerformed() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup: Assigning the histogram to data
actionPerformed() - Method in class etomica.models.oneDHardRods.WriteHistograms
actionPerformed() - Method in class etomica.modifier.ModifyAction: Executes the setValue method of the wrapped modifier, using the value given in the most recent call to this.setValue.
actionPerformed(ActionEvent) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
actionPerformed(ActionEvent) - Method in class etomica.modules.clustergenerator.MyApplet.Stopper
actionPerformed() - Method in class etomica.modules.colloid.ColloidGraphic.GraftAction
actionPerformed() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
actionPerformed() - Method in class etomica.modules.pistoncylinder.ActionPistonUpdate
actionPerformed() - Method in class etomica.modules.sam.SamGraphic.ActionMoveWall
actionPerformed() - Method in class etomica.normalmode.HSNPT.ActionSummer
actionPerformed() - Method in class etomica.normalmode.MeterAtomicDisplacement
actionPerformed() - Method in class etomica.normalmode.MeterNormalMode: Calculating things and adds terms to the sums
actionPerformed() - Method in class etomica.normalmode.MeterTiltHistogram
actionPerformed() - Method in class etomica.normalmode.MeterTiltRotationHistogram
actionPerformed() - Method in class etomica.normalmode.WriteS
actionPerformed(IAtom) - Method in class etomica.paracetamol.AtomActionTransformed
actionPerformed() - Method in class etomica.surfacetension.ActionRecenter
actionPerformed(ActionEvent) - Method in class etomica.util.Grabber.ActionCornerSetter
actionPerformed(IEvent) - Method in interface etomica.util.IListener
actionPerformed() - Method in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
actionPerformed() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
actionPerformed(ActionEvent) - Method in class etomica.veos.bigdecimal.Wigner3jGUI: Interpreter parser loop.
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBox.CloseWindowButtonListener
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
actionPerformed() - Method in class etomica.virial.MeterVirialBDBin
actionPerformed() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
actionPerformed() - Method in class etomica.virial.MeterVirialBinMultiThreaded
actionPerformed() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
actionPerformed(IMolecule) - Method in class etomica.virial.MoleculeActionRelaxWater3P
actionPerformed() - Method in class etomica.zeolite.MSDCoordWriter
actionPerformed(IEvent) - Method in class etomica.zeolite.MSDCoordWriter
actionPerformed() - Method in class etomica.zeolite.ZeoliteSimStart
ActionPistonUpdate - Class in etomica.modules.pistoncylinder: Action that informs the integrator that some property of the piston has changed (pressure, mass, velocity)
ActionPistonUpdate(IntegratorHardPiston) - Constructor for class etomica.modules.pistoncylinder.ActionPistonUpdate
ActionRecenter - Class in etomica.surfacetension
ActionRecenter(LJMC) - Constructor for class etomica.surfacetension.ActionRecenter
actions - Variable in class etomica.action.activity.ActivityGroupParallel
ActionSet() - Constructor for class etomica.graphics.Device.ActionSet
ActionStatus(String) - Constructor for class etomica.action.activity.Controller.ActionStatus
actionStatusMap - Variable in class etomica.action.activity.Controller
ActionSummer(IBox, ISpace) - Constructor for class etomica.normalmode.HSNPT.ActionSummer
ActionToggle - Class in etomica.action: Action that toggles a boolean value.
ActionToggle(ModifierBoolean) - Constructor for class etomica.action.ActionToggle
ActionToggle(ModifierBoolean, String, String) - Constructor for class etomica.action.ActionToggle
ActionVelocityWindow - Class in etomica.graphics: Action that opens a new window and dumps the velocities into the window.
ActionVelocityWindow(IBox) - Constructor for class etomica.graphics.ActionVelocityWindow
active - Variable in class etomica.data.DataAccumulator: Flag specifying whether the manager responds to integrator events
active - Variable in class etomica.threaded.atom.PotentialMasterListWorker
active - Variable in class etomica.threaded.domain.PotentialMasterListWorker
activeCornerSetter - Variable in class etomica.util.Grabber
Activity - Class in etomica.action: An Action that supports the capability of pausing/unpausing and terminating on request.
Activity() - Constructor for class etomica.action.Activity: Create class with a simple default label.
Activity(Activity) - Constructor for class etomica.action.Activity: Copy constructor.
activity - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
activity - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
ActivityGroup - Interface in etomica.action.activity
ActivityGroupParallel - Class in etomica.action.activity: Organizer of simulation actions to be executed in parallel, each on its own thread.
ActivityGroupParallel() - Constructor for class etomica.action.activity.ActivityGroupParallel
ActivityGroupParallel(IAction[]) - Constructor for class etomica.action.activity.ActivityGroupParallel
ActivityGroupSeries - Class in etomica.action.activity: Organizer of simulation actions to be executed in series.
ActivityGroupSeries() - Constructor for class etomica.action.activity.ActivityGroupSeries
ActivityIntegrate - Class in etomica.action.activity: Activity that repeatedly invokes an Integrator's doStep method.
ActivityIntegrate(IIntegrator) - Constructor for class etomica.action.activity.ActivityIntegrate: Constructs activity to generate configurations with the given integrator (which is final).
ActivityIntegrate(IIntegrator, int, boolean) - Constructor for class etomica.action.activity.ActivityIntegrate
activityIntegrate - Variable in class etomica.AlkaneEH.CH4NVT
activityIntegrate - Variable in class etomica.AlkaneEH.DHS_NVT
activityIntegrate - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
activityIntegrate - Variable in class etomica.densityofstate.DensityOfState
activityIntegrate - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
activityIntegrate - Variable in class etomica.dielectric.DHS_NVT
activityIntegrate - Variable in class etomica.dielectric.DLJ_NVT_1site
activityIntegrate - Variable in class etomica.dielectric.TIP4P_NVT
activityIntegrate - Variable in class etomica.dimer.IntegratorDimerMin
activityIntegrate - Variable in class etomica.dimer.IntegratorDimerRT
activityIntegrate - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
activityIntegrate - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
activityIntegrate - Variable in class etomica.mappedvirial.MappedU
activityIntegrate - Variable in class etomica.mappedvirial.MappedVirialLJ
activityIntegrate - Variable in class etomica.mappedvirial.MappedVirialLJVGr
activityIntegrate - Variable in class etomica.meam.EFSTungsten
activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithGB
activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
activityIntegrate - Variable in class etomica.meam.MEAM_MC
activityIntegrate - Variable in class etomica.meam.MEAMMd3D
activityIntegrate - Variable in class etomica.metastable.LJmuVT
activityIntegrate - Variable in class etomica.metastable.LJNPT
activityIntegrate - Variable in class etomica.metastable.LJNVT
activityIntegrate - Variable in class etomica.models.hexane.HexaneVolumeFraction
activityIntegrate - Variable in class etomica.models.hexane.SimHarmonicHexane
activityIntegrate - Variable in class etomica.models.hexane.TestHexane
activityIntegrate - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
activityIntegrate - Variable in class etomica.models.hexane.TestHexaneFileConfig
activityIntegrate - Variable in class etomica.models.hexane.TestHexaneHarmonic
activityIntegrate - Variable in class etomica.models.hexane.TestSetToUHexane
activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
activityIntegrate - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
activityIntegrate - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
activityIntegrate - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
activityIntegrate - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImage
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
activityIntegrate - Variable in class etomica.models.oneDHardRods.SimWidomMode
activityIntegrate - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
activityIntegrate - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
activityIntegrate - Variable in class etomica.modules.adsorption.Adsorption
activityIntegrate - Variable in class etomica.modules.catalysis.Catalysis
activityIntegrate - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
activityIntegrate - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
activityIntegrate - Variable in class etomica.modules.colloid.ColloidSim
activityIntegrate - Variable in class etomica.modules.dcvgcmd.DCVGCMD
activityIntegrate - Variable in class etomica.modules.droplet.Droplet
activityIntegrate - Variable in class etomica.modules.droplet.DropletAtomic
activityIntegrate - Variable in class etomica.modules.ensembles.LJMC
activityIntegrate - Variable in class etomica.modules.entropylottery.EntropyLottery
activityIntegrate - Variable in class etomica.modules.insertion.Insertion
activityIntegrate - Variable in class etomica.modules.interfacial.InterfacialSW
activityIntegrate - Variable in class etomica.modules.ljmd.Ljmd
activityIntegrate - Variable in class etomica.modules.mu.Mu
activityIntegrate - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
activityIntegrate - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
activityIntegrate - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
activityIntegrate - Variable in class etomica.modules.osmosis.OsmosisSim
activityIntegrate - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
activityIntegrate - Variable in class etomica.modules.render.RenderMD
activityIntegrate - Variable in class etomica.modules.rheology.SimulationRheology
activityIntegrate - Variable in class etomica.modules.rosmosis.ReverseOsmosis
activityIntegrate - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
activityIntegrate - Variable in class etomica.modules.sam.Sam
activityIntegrate - Variable in class etomica.modules.swmd.Swmd
activityIntegrate - Variable in class etomica.modules.vle.VLESim
activityIntegrate - Variable in class etomica.normalmode.HessianDB
activityIntegrate - Variable in class etomica.normalmode.HSDimerNPT
activityIntegrate - Variable in class etomica.normalmode.HSNPT
activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
activityIntegrate - Variable in class etomica.normalmode.SimBennet
activityIntegrate - Variable in class etomica.normalmode.SimCalcJ
activityIntegrate - Variable in class etomica.normalmode.SimCalcS
activityIntegrate - Variable in class etomica.normalmode.SimCalcSLJ
activityIntegrate - Variable in class etomica.normalmode.SimCalcSMorse
activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
activityIntegrate - Variable in class etomica.normalmode.SimEinStep1
activityIntegrate - Variable in class etomica.normalmode.SimEinStep1HCP
activityIntegrate - Variable in class etomica.normalmode.SimEinStep2
activityIntegrate - Variable in class etomica.normalmode.SimEinStep2HCP
activityIntegrate - Variable in class etomica.normalmode.SimFluidSoftSphere
activityIntegrate - Variable in class etomica.normalmode.SimHarmonic
activityIntegrate - Variable in class etomica.normalmode.SimHarmonicUmbrella
activityIntegrate - Variable in class etomica.normalmode.SimLJHTTISuper
activityIntegrate - Variable in class etomica.normalmode.SimLJHTTISuperHCP
activityIntegrate - Variable in class etomica.normalmode.SimModesJ
activityIntegrate - Variable in class etomica.normalmode.SimOverlap
activityIntegrate - Variable in class etomica.normalmode.SimOverlapLJ
activityIntegrate - Variable in class etomica.normalmode.SimOverlapLJModule
activityIntegrate - Variable in class etomica.normalmode.SimOverlapModule
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphere
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
activityIntegrate - Variable in class etomica.normalmode.SimOverlapSSnxy
activityIntegrate - Variable in class etomica.normalmode.SimTarget
activityIntegrate - Variable in class etomica.normalmode.SimTargetUmbrella
activityIntegrate - Variable in class etomica.normalmode.SimUmbrella
activityIntegrate - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
activityIntegrate - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
activityIntegrate - Variable in class etomica.surfacetension.LJMC
activityIntegrate - Variable in class etomica.threaded.atom.LJMD3DThreaded
activityIntegrate - Variable in class etomica.threaded.domain.LJMD3DThreaded
activityIntegrate - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
activityIntegrate - Variable in class etomica.zeolite.ZeoliteSimulation
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerLJadatom
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerLJgb
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerMEAMadatom
activityIntegrateDimer - Variable in class etomica.dimer.SimDimerMEAMGB
activityIntegrateDimer - Variable in class etomica.kmc.SimKMCLJadatom
activityIntegrateDimer - Variable in class etomica.kmc.SimKMCMEAMadatom
activityIntegrateKMC - Variable in class etomica.kmc.SimKMCLJadatom
activityIntegrateKMC - Variable in class etomica.kmc.SimKMCMEAMadatom
activityIntegrateKMCCluster - Variable in class etomica.kmc.SimKMCLJadatom
activityIntegrateKMCCluster - Variable in class etomica.kmc.SimKMCMEAMadatom
activityIntegrateMAP - Variable in class etomica.dimer.EnergyMap
activityIntegrateMD - Variable in class etomica.dimer.SimDimerLJadatom
activityIntegrateMD - Variable in class etomica.dimer.SimDimerLJgb
activityIntegrateMD - Variable in class etomica.dimer.SimDimerMEAMadatom
activityIntegrateMD - Variable in class etomica.dimer.SimDimerMEAMGB
activityIntegrateMin - Variable in class etomica.dimer.SimDimerLJadatom
activityIntegrateMin - Variable in class etomica.dimer.SimDimerMEAMadatom
activityIntegrateMin - Variable in class etomica.dimer.SimDimerMEAMGB
actualFlipList - Variable in class etomica.virial.ClusterCoupledFlippedPartial
acType - Variable in class etomica.models.rowley.SpeciesEthanol
acType - Variable in class etomica.models.rowley.SpeciesMethanol
adAtomPos - Variable in class etomica.dimer.SimDimerLJadatom
adAtomPos - Variable in class etomica.dimer.SimDimerMEAMadatom
adAtomPos - Variable in class etomica.dimer.SimDimerMEAMGB
adAtomPos - Variable in class etomica.kmc.SimKMCLJadatom
adAtomPos - Variable in class etomica.kmc.SimKMCMEAMadatom
add(IAtom) - Method in class etomica.atom.AtomArrayList
add(IMolecule) - Method in class etomica.atom.MoleculeArrayList
add(Feature) - Method in class etomica.compatibility.FeatureSet
add(String, String) - Method in class etomica.compatibility.FeatureSet
add(String, double) - Method in class etomica.compatibility.FeatureSet
add(Requirement) - Method in class etomica.compatibility.RequirementSet
add(Coefficient) - Method in interface etomica.graph.model.Coefficient
add(E) - Method in class etomica.graph.model.GraphList
add(Coefficient) - Method in class etomica.graph.model.impl.CoefficientImpl
add(Display) - Method in class etomica.graphics.SimulationGraphic
add(Device) - Method in class etomica.graphics.SimulationGraphic: Adds displays graphic to the simulation display pane
add(P2HardBondedList.MyBond) - Method in class etomica.potential.P2HardBondedList.BondArrayList
add(IFunction) - Method in class etomica.util.FunctionChain: Adds the given function to the chain of functions.
add(Object) - Method in class etomica.util.ObjectArrayList: Appends the specified element to the end of this list.
add(int, Object) - Method in class etomica.util.ObjectArrayList: Inserts the specified element at the specified position in this list.
add(TreeLinker) - Method in class etomica.util.TreeList
add(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Add a BigDecimal and a BigInteger.
add(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Add another polynomial
add(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd: Add two surds of compatible discriminant.
add(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec: Add two vectors algebraically.
add(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec: Add two vectors algebraically.
add(BigInteger) - Method in class etomica.veos.bigdecimal.Ifactor: Summation with another positive integer
add(Rational) - Method in class etomica.veos.bigdecimal.Rational: Add another fraction.
add(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Add another integer.
add(int) - Method in class etomica.veos.bigdecimal.Rational: Add another integer.
add(Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to sum of itself and matrix m1.
add(float) - Method in class org.jmol.util.Quaternion
add(Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the vector sum of itself and tuple t1.
add(Tuple3i) - Method in class org.jmol.util.Tuple3i: Sets the value of this tuple to the sum of itself and t1.
add2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the vector sum of tuples t1 and t2.
ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JmolConstants
addAction(IAction) - Method in interface etomica.action.ActionGroup: Adds the given newAction to this group.
addAction(IAction) - Method in class etomica.action.ActionGroupSeries: Adds the given action to the group.
addAction(IAction) - Method in class etomica.action.activity.ActivityGroupParallel
addAction(IAction) - Method in class etomica.action.activity.ActivityGroupSeries: Adds the given action to the list of actions.
addAction(IAction) - Method in class etomica.action.activity.Controller
addAddSpecies1ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addAddSpecies2ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addAddSpecies3ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addAgent(IAtom) - Method in class etomica.atom.AtomLeafAgentManager: Adds an agent for the given leaf atom to the agents array.
addAgent(IAtom, int) - Method in class etomica.atom.AtomLeafAgentManager: Adds an agent for the given leaf atom to the agents array at the given index.
addAgent(IAtomType) - Method in class etomica.atom.AtomTypeAgentManager
addAgent(IMolecule) - Method in class etomica.atom.MoleculeAgentManager
addAgent(ISpecies) - Method in class etomica.atom.SpeciesAgentManager
addAgent(IBox) - Method in class etomica.box.BoxAgentManager
addAlkaneLengthViewListener(int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
addAll(IAtomList) - Method in class etomica.atom.AtomArrayList
addAll(IMoleculeList) - Method in class etomica.atom.MoleculeArrayList
addAll(Collection<? extends E>) - Method in class etomica.graph.model.GraphList
addAlterSimEnvButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addAlterSimEnvButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addAnotherSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addAsTab(Component, String, boolean) - Method in class etomica.graphics.SimulationGraphic
addAtom(IAtom) - Method in class etomica.nbr.cell.Cell
addAtomNotify(IAtom) - Method in class etomica.nbr.list.NeighborListManager: Constructs neighbor lists for the given atom
addAtomNotify(IAtom) - Method in class etomica.nbr.list.NeighborListManagerSlanty: Constructs neighbor lists for the given atom
addAuthor(String) - Method in class etomica.graphics.DefaultToolbar
addBDOne(BigDecimal) - Static method in class etomica.data.types.DataDoubleBDArray
addBDZero(BigDecimal) - Static method in class etomica.data.types.DataDoubleBDArray
addBondedPotentialSets(CollectionPotentialAtomicLike, ISpace, int) - Method in class etomica.virial.GUI.components.ACollectionBondedPotential
addBondedPotentialSets(CollectionPotentialAtomicLike, ISpace, int) - Method in class etomica.virial.GUI.components.CollectionBondedPotentialAlcohols
addBondedPotentialSets(CollectionPotentialAtomicLike, ISpace, int) - Method in class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
addBoundBoxPoint(Point3f) - Method in class org.jmol.util.BoxInfo
addBox(IBox) - Method in interface etomica.api.ISimulation: Adds a Box to the simulation.
addBox(IBox) - Method in class etomica.simulation.Simulation
addButton(String, IAction) - Method in class etomica.graphics.DeviceButtonGroup: Adds a radio button with the given label, which (when selected) performs the given action.
addCellNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Add the specified listener to the list of listeners that will get invoked when the 'nCell #' slider value changes.
addChangeableWV(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
addChangeableWV(String) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
addChildAtom(IAtom) - Method in class etomica.atom.Molecule: Adds the given Atom as a child of this Atom.
addChildType(IAtomType) - Method in class etomica.species.Species
addChildType(IAtomType) - Method in class etomica.species.SpeciesSpheresHetero: Adds the given factory as a child of this factory.
addChooseOkayButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
addCluster(ClusterDiagram) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
addClusterDiagram(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagramTree: Adds the given diagram to the tree, adding nodes as needed
addCollisionListener(IntegratorHard.CollisionListener) - Method in class etomica.integrator.IntegratorHard: Registers an object that implements the CollisionListener interface.
addComparator(Comparator<Graph>) - Method in class etomica.graph.model.comparators.ComparatorChain: Add a comparator that will be used to sort sort graphs.
addComponent(Component, JPanel, int, int, int, int) - Method in class etomica.modules.clustergenerator.MyApplet: Componet c is added to JPanel panel following the rule of GridBagLayout manager
addConnection(int, int) - Method in class etomica.virial.cluster.ClusterDiagram: Adds a connection between the node1 and node2.
addContributor(String) - Method in class etomica.graphics.DefaultToolbar
addCountOfSpeciesSLMListener(ChangeListener, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addCriterion(IteratorDirective.PotentialCriterion) - Method in class etomica.atom.iterator.IteratorDirective: Adds criterion to set of criteria for potentials.
addData(IData) - Method in class etomica.data.AccumulatorAverageBlockless: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageBlocklessSlim: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsing: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLog: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageCovariance
addData(IData) - Method in class etomica.data.AccumulatorAverageFixed: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorAverageFixedOutputFile: Add the given values to the sums and block sums.
addData(IData) - Method in class etomica.data.AccumulatorCounter: Increments the counter.
addData(IData) - Method in class etomica.data.AccumulatorHistogram: Adds each value in the given Data to its own histogram.
addData(IData) - Method in class etomica.data.AccumulatorHistory: Adds each value in the given array to its own history.
addData(IData) - Method in class etomica.data.DataAccumulator: Defined by subclass to specify what this accumulator does when data is added to it.
addData(BigDecimal, MathContext) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
addData(double) - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
addData(double[]) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
addData(double[]) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
addData(IData) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: Add the given values to the sums and block sums
addDataListener(DataSetListener) - Method in class etomica.data.DataSet
addDataSink(IDataSink, AccumulatorAverage.StatType[]) - Method in class etomica.data.AccumulatorAverage: Adds a new DataSink that will receive a specific subset of the statistics generated by this accumulator.
addDataSink(IDataSink, AccumulatorAverageBlockless.StatType[]) - Method in class etomica.data.AccumulatorAverageBlockless: Adds a new DataSink that will receive a specific subset of the statistics generated by this accumulator.
addDataSink(IDataSink) - Method in class etomica.data.DataFork
addDataSink(IDataSink) - Method in interface etomica.data.DataPipeForked: Adds the given DataSink to those receiving the Data entering this DataFork, keeping all previously entered DataSinks.
addDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked: Adds the given DataSink to those receiving the Data entering this DataFork, keeping all previously entered DataSinks.
addDataSource(IEtomicaDataSource) - Method in class etomica.data.DataSourceGroup: Adds the given DataSource to those held by the group.
addDataSource(IEtomicaDataSource) - Method in class etomica.data.DataTableAverages: Adds the given data source to those feeding the table.
addDownNbr(IAtom, int) - Method in class etomica.nbr.list.AtomNeighborLists: Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addDownNbr(IMolecule, int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists: Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addDrawable(Drawable) - Method in class etomica.graphics.DisplayBox
addDrawable(Object) - Method in class etomica.graphics.DisplayBox
addEditVariablesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addEditVariablesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addEquivalents(ArrayList<ClusterDiagram>) - Static method in class etomica.virial.cluster.ClusterOperations: Replaces all isomorphic clusters in the given list by a single cluster with weight given by their sum.
addEValNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Add the specified listener to the list of listeners that will get invoked when the 'eigenvalues #' slider value changes.
addFactors(int[]) - Method in interface etomica.graph.model.Graph
addFactors(int[]) - Method in class etomica.graph.model.impl.GraphImpl
addFig(Figure) - Method in class g3dsys.control.G3DSys: Adds the Figure to the associated FigureManager
addFilter(String) - Method in class etomica.graph.engine.impl.ConstructorImpl
addFilter(String) - Method in interface etomica.graph.engine.Parser.Constructor
addIntegrator(IIntegrator) - Method in class etomica.integrator.IntegratorGEMC
addIntegrator(IIntegrator) - Method in class etomica.integrator.IntegratorManagerMC
addIntegrator(IntegratorBox) - Method in class etomica.integrator.IntegratorPT: Adds the given integrator to those managed by this integrator, and includes integrator's box to the set among which configurations are swapped.
addIntersectionVertex(Point3f, float, int, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSurface
additive - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
addLine(LineSegment) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
addListener(IBoundaryListener) - Method in interface etomica.api.IBoundaryEventManager: Adds the given listener to this event manager.
addListener(IBoxListener) - Method in interface etomica.api.IBoxEventManager: Adds the given listener to this event manager.
addListener(IIntegratorListener) - Method in interface etomica.api.IIntegratorEventManager: Adds the given listener to this event manager.
addListener(ISimulationListener) - Method in interface etomica.api.ISimulationEventManager
addListener(IBoxListener) - Method in class etomica.box.BoxEventManager
addListener(DeviceTernarySelector.Listener) - Method in class etomica.graphics.DeviceTernarySelector
addListener(IIntegratorListener) - Method in class etomica.integrator.IntegratorEventManager
addListener(IIntegratorListener) - Method in class etomica.listener.IntegratorListenerGroupSeries: Adds the given action to the group.
addListener(IListener) - Method in interface etomica.listener.ListenerGroup: Adds the given newAction to this group.
addListener(INeighborListListenerMolecular) - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
addListener(INeighborListListener) - Method in class etomica.nbr.list.NeighborListEventManager
addListener(ISimulationListener) - Method in class etomica.simulation.SimulationEventManager
addListener(IBoundaryListener) - Method in class etomica.space.BoundaryEventManager
addListener(IListener) - Method in class etomica.util.EventManager
addListener(IListener, boolean) - Method in class etomica.util.EventManager
addListener(IListener) - Method in interface etomica.util.IEventManager: Adds the given listener to this event manager.
addMCMove(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager: Adds the given MCMove to the set of moves performed by the integrator and recalculates move frequencies.
addModel(Model) - Method in interface etomica.api.IPotentialMaster: Add the given Model's intramolecular potentials to this PotentialMaster
addModel(Model) - Method in class etomica.graphics.BondListener: Infroms the BondListener that is should track bonds associated with all molecules of the given Model.
addModel(Model) - Method in class etomica.potential.PotentialMaster
addMolecule(IMolecule) - Method in interface etomica.api.IBox: Adds the given molecule to the this box.
addMolecule(IMolecule) - Method in class etomica.box.Box
addMolecule(IMolecule) - Method in class etomica.nbr.cell.molecule.CellMolecular
addMoleculeListDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addMoleculeListDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addMoleculeNotify(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Constructs neighbor lists for the given atom
addMoleculeNotify(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular: Constructs neighbor lists for the given molecule
addNewMolecule(ISpecies) - Method in class etomica.box.Box
addNoDoNotRemoveSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
addObject(Object[], Object) - Static method in class etomica.util.Arrays: Returns an array formed from adding the newObject to the elements in the given array.
addOption(String, IAction) - Method in class etomica.graphics.DeviceSelector
addPair(NodePair) - Method in interface etomica.graph.isomorphism.SearchState
addPair(NodePair) - Method in class etomica.graph.isomorphism.UllmanSearchState
addPair(NodePair) - Method in class etomica.graph.isomorphism.VF2SearchState
addPair(NodePair) - Method in class etomica.graph.isomorphism.VFSearchState
addParser(ParameterParser) - Method in class etomica.util.ParameterBase
addPlane(Plane) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
addPoint(Point3f, Point3f, Point3f, float) - Static method in class org.jmol.util.BoxInfo
addPointXYZ(float, float, float, Point3f, Point3f, float) - Static method in class org.jmol.util.BoxInfo
addPolygonC(int[], int, BitSet) - Method in class org.jmol.util.MeshSurface
addPotential(IPotentialMolecular, ISpecies[]) - Method in interface etomica.api.IPotentialMaster: Indicates to the PotentialMaster that the given potential should apply to the specified species.
addPotential(IPotentialAtomic, IAtomType[]) - Method in interface etomica.api.IPotentialMaster: Indicates to the PotentialMaster that the given potential should apply to the specified atom types.
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, IAtomType[]) - Method in class etomica.nbr.PotentialGroupNbr
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.PotentialMasterHybrid
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.PotentialMasterNbr
addPotential(IPotential) - Method in class etomica.potential.PotentialArray: Identifies the given potential to this type instance and returns the index assigned to it.
addPotential(IPotential, IAtomType) - Method in class etomica.potential.PotentialArrayByType: Identifies the given potential to this type instance and returns the index assigned to it.
addPotential(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular: Identifies the given potential to this type instance and returns the index assigned to it.
addPotential(IPotentialAtomic, IAtomType[]) - Method in class etomica.potential.PotentialGroup: Adds the given potential and sets it up to apply to the atoms in the basis having the given types.
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent) - Method in class etomica.potential.PotentialGroup: Adds the given potential to this group, defining it to apply to the atoms provided by the given basis-dependent iterator.
addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, IAtomType[]) - Method in class etomica.potential.PotentialGroup
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.potential.PotentialMaster
addPotential(IPotentialAtomic, IAtomType[]) - Method in class etomica.potential.PotentialMaster
addPotential(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) - Method in class etomica.potential.PotentialMaster
addPotential(IPotentialMolecular) - Method in class etomica.potential.PotentialMasterLrc
addPotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMasterLrc
addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.potential.PotentialMasterMonatomic
addPotential(IPotentialAtomic, IAtomType[]) - Method in class etomica.potential.PotentialMasterMonatomic
addPotentialButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addPotentialButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addPotentialNbrList(IPotentialAtomic, IAtomType[], NeighborCriterion) - Method in class etomica.nbr.list.PotentialMasterList: Add the given potential to be used for the given atom types and the given criterion.
addPotentialsJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addPotentialsJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addPotParamDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addPotParamDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addPotParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addPotParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addProgressListener(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2: Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation.
addProgressListener(double, boolean) - Method in class etomica.virial.simulations.SimulationVirialOverlap2: Causes a progress report (coefficient value and uncertainty) 10 times during the course of the simulation.
addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.util.Grabber.ActionCornerSetter
addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
addRadioGroupActionListener(ActionListener) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Add the specified listener to the list of listeners that will get invoked when the isothermal or adiabatic radio button is pushed.
addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Add the specified listener to the list of listeners that will get invoked when the "x-axis" or "y-axis" radio button is pushed.
addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Add the specified listener to the list of listeners that will get invoked when the "Eigenvalue" or "All Eigenvalues" radio button is pushed.
addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Add the specified listener to the list of listeners that will get invoked when the "Wave Vector" or "All Wave Vectors" radio button is pushed.
addRangedPotential(IPotentialMolecular, ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
addRangedPotential(IPotentialAtomic, IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Adds the potential as a ranged potential that applies to the given AtomTypes.
addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.list.PotentialMasterList: Adds the potential as a ranged potential that applies to the given AtomTypes.
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.PotentialMasterHybrid
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.PotentialMasterNbr
addRangedPotentialForTypes(IPotentialAtomic, IAtomType[]) - Method in class etomica.nbr.site.PotentialMasterSite
addRemoveButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addRemoveSpecies1ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addRemoveSpecies2ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addRemoveSpecies3ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addResetButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addResetButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addReverseComparator(Comparator<Graph>) - Method in class etomica.graph.model.comparators.ComparatorChain: Add a comparator that will be used to sort sort graphs in reverse order.
addRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Add and round according to the larger of the two ulp's.
addRound(BigComplex, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Add and round according to the larger of the two ulp's.
addRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Add and round according to the larger of the two ulp's.
addRunButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addRunButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addSameSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addSaveValuesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
addSaveValuesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
addSpecies(ISpecies) - Method in interface etomica.api.ISimulation: Adds species to the list of all ISpecies in the simulation, and adds notifies all IBoxes of the new ISpecies.
addSpecies(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
addSpecies(ISpecies) - Method in class etomica.simulation.Simulation
addSpecies(Object) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
addSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addSpeciesIndextoSites(String[], int) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
addSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
addSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
addSpeciesMolecule(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
addSpeciesNotify(ISpecies) - Method in interface etomica.api.IBox: Notifies the IBox that the given species has been added to the simulation.
addSpeciesNotify(ISpecies) - Method in class etomica.box.Box
addStateChangedListener(ChangeListener) - Method in class etomica.modules.osmosis.Osmosis.InitializeMolecules
addTag(DataTag) - Method in class etomica.data.DataInfo: Adds the tag
addTag(DataTag) - Method in interface etomica.data.IEtomicaDataInfo: Adds the tag to this IDataInfo object.
addTag(DataTag) - Method in class etomica.data.types.DataGroup.DataInfoGroup
addTags(DataTag[]) - Method in class etomica.data.DataInfo: Convenience method to add all of the given tags.
addTags(DataTag[]) - Method in interface etomica.data.IEtomicaDataInfo: Convenience method to add all of the given tags.
addTags(DataTag[]) - Method in class etomica.data.types.DataGroup.DataInfoGroup
addTemperatureSliderListener(ChangeListener) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Add the specified listener to the list of listeners that will get invoked when the temperature slider value changes.
addTensor(int, Tensor) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile: Adds the given contribution to the virial sum for bin iBin.
addThermostatAction(IAction) - Method in class etomica.normalmode.IntegratorHardMDMC
addToHashMapPotentialNonBonded(String[], IPotential) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
addToHashMapPotentialNonBonded(String[], IPotential) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
addToken(String, Token) - Static method in class org.jmol.script.Token
addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
addUpNbr(IAtom, int) - Method in class etomica.nbr.list.AtomNeighborLists: Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addUpNbr(IMolecule, int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists: Adds the given atom as a "down" neighbor interacting via the potential with the given index.
addValue(double) - Method in interface etomica.util.Histogram: Adds the given value to the Histogram
addValue(double) - Method in class etomica.util.HistogramCollapsing
addValue(double) - Method in class etomica.util.HistogramDiscrete
addValue(double) - Method in class etomica.util.HistogramExpanding
addValue(double, double) - Method in class etomica.util.HistogramNotSoSimple
addValue(double) - Method in class etomica.util.HistogramNotSoSimple
addValue(double, double) - Method in class etomica.util.HistogramReweightedData
addValue(double) - Method in class etomica.util.HistogramReweightedData
addValue(double) - Method in class etomica.util.HistogramSimple
addValue(double, double) - Method in interface etomica.util.History: Adds the given x, y pair to the History.
addValue(double, double) - Method in class etomica.util.HistoryCollapsingAverage: adds data to the history.
addValue(double, double) - Method in class etomica.util.HistoryCollapsingDiscard: adds data to the history.
addValue(double, double) - Method in class etomica.util.HistoryComplete
addValue(double, double) - Method in class etomica.util.HistoryScrolling
addValueChangedListener(DeviceBoxValueChangedListener) - Method in class etomica.graphics.DeviceBox: Add an object to be notified when the DeviceBox value to changes
addVertexCopy(Point3f) - Method in class org.jmol.util.MeshSurface
addVertexCopy(Point3f, float, boolean, int) - Method in class org.jmol.util.MeshSurface
addVertexCopyVal(Point3f, float) - Method in class org.jmol.util.MeshSurface
addWaveVectorNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Add the specified listener to the list of listeners that will get invoked when the 'wave vectors #' slider value changes.
addXYCellNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Add the specified listener to the list of listeners that will get invoked when the 'xCell #' and 'yCell #' slider value changes.
addYesRemoveSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
aDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
aDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
aDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
adjustCountdown - Variable in class etomica.overlap.IntegratorOverlap
adjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
adjustInterval - Variable in class etomica.overlap.IntegratorOverlap
adjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
adjustStepFreq() - Method in class etomica.virial.overlap.IntegratorOverlap: Adjusts the frequency with which steps for each sub-integrator are performed.
adjustStepFreq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
adjustStepFreq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
adjustStepSize() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
adpmax - Static variable in class org.jmol.script.Token
adpmin - Static variable in class org.jmol.script.Token
Adsorption - Class in etomica.modules.adsorption: Simulation for Adsorption module.
Adsorption(ISpace) - Constructor for class etomica.modules.adsorption.Adsorption
AdsorptionGraphic - Class in etomica.modules.adsorption: Catalysis graphical app.
AdsorptionGraphic(Adsorption, ISpace) - Constructor for class etomica.modules.adsorption.AdsorptionGraphic
AdsorptionGraphic.Applet - Class in etomica.modules.adsorption
advance() - Method in class etomica.graph.iterators.CartesianIterator
advance() - Method in class etomica.graph.iterators.CartesianPermutator
advance() - Method in class etomica.virial.cluster.ClusterGenerator: Advances the cluster to the next cluster matching the given criteria.
advanceAcrossTimeStep(double) - Method in class etomica.integrator.IntegratorHard: Advances all atom coordinates by tStep, without any intervening collisions.
advanceAcrossTimeStep(double) - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
advanceAcrossTimeStep(double) - Method in class etomica.potential.P1HardMovingBoundary
advanceParameters() - Method in class etomica.thermointegration.IntegratorThermodynamic: Method to advance the thermodynamic parameter(s) of interest as part of the thermodynamic integration.
advanceParameters() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
aEE - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
aEE - Variable in class etomica.dielectric.TIP4P_NVT.Param
Aelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
aErr - Variable in class etomica.potential.P2HePCKLJS
aFe - Variable in class etomica.meam.PotentialFeEAM_LS
affectedAtomIterator - Variable in class etomica.association.MCMoveDimer
affectedAtomIterator - Variable in class etomica.association.MCMoveDimerRotate
affectedAtomIterator - Variable in class etomica.association.MCMoveSmer
affectedAtomIterator - Variable in class etomica.association.MCMoveSmerRotate
affectedAtomIterator - Variable in class etomica.association.MCMoveVolumeAssociated
affectedAtomIterator - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
affectedAtomIterator - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
affectedAtomIterator - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveAtom
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveDimer
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveMolecule
affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveVolume
affectedAtomIterator - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
affectedAtomIterator - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupled
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomSuperBox
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeSolid
affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
affectedAtomIterator - Variable in class etomica.spin.MCMoveSpinFlip
affectedAtomIterator - Variable in class etomica.virial.MCMoveClusterAngleBend
affectedAtomIterator - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupled
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomSuperBox
affectedAtoms() - Method in class etomica.association.MCMoveBiasUB
affectedAtoms() - Method in class etomica.association.MCMoveBiasUBMolecule
affectedAtoms - Variable in class etomica.association.MCMoveDimer
affectedAtoms() - Method in class etomica.association.MCMoveDimer
affectedAtoms - Variable in class etomica.association.MCMoveDimerRotate
affectedAtoms() - Method in class etomica.association.MCMoveDimerRotate
affectedAtoms() - Method in class etomica.association.MCMoveSmer
affectedAtoms() - Method in class etomica.association.MCMoveSmerRotate
affectedAtoms() - Method in class etomica.association.MCMoveVolumeAssociated
affectedAtoms() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
affectedAtoms() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
affectedAtoms() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
affectedAtoms() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMove: Returns an iterator that yields the atoms that were affected by the trial move the last time doTrial was invoked (regardless of whether the move was accepted).
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveAtom
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveBox
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveBox
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
affectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveDimer
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveDimer
affectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Returns an iterator giving molecule that is being added or deleted in the current or most recent trial.
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveMolecule
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveVolume
affectedAtoms(IBox) - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
affectedAtoms() - Method in class etomica.models.hexane.MCMoveCBMC
affectedAtoms() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
affectedAtoms() - Method in class etomica.models.hexane.MCMoveReptate
affectedAtoms() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
affectedAtoms() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
affectedAtoms() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
affectedAtoms() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
affectedAtoms() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
affectedAtoms() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
affectedAtoms() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
affectedAtoms() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupled
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomSuperBox
affectedAtoms() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
affectedAtoms() - Method in class etomica.normalmode.MCMoveHarmonic
affectedAtoms() - Method in class etomica.normalmode.MCMoveHarmonicStep
affectedAtoms() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
affectedAtoms() - Method in class etomica.normalmode.MCMovePhaseAngle
affectedAtoms() - Method in class etomica.normalmode.MCMoveSingleMode
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeSolid
affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
affectedAtoms() - Method in class etomica.normalmode.MCMoveWV
affectedAtoms() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
affectedAtoms() - Method in class etomica.spin.MCMoveSpinFlip
affectedAtoms() - Method in class etomica.virial.MCMoveChangeBondLength
affectedAtoms() - Method in class etomica.virial.MCMoveClusterAngleBend
affectedAtoms() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
affectedAtoms() - Method in class etomica.virial.MCMoveClusterAtomQ
affectedAtoms(IBox) - Method in class etomica.virial.MCMoveClusterAtomQ
affectedAtoms() - Method in class etomica.virial.MCMoveClusterDiagram
affectedAtoms() - Method in class etomica.virial.MCMoveClusterReptateMulti
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrow
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingScale
affectedAtoms(IBox) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
affectedMol - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
affectedMoleculeIterator - Variable in class etomica.association.MCMoveBiasUBMolecule
affectedMoleculeIterator - Variable in class etomica.integrator.mcmove.MCMoveMolecule
affectedMoleculeIterator - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
affectedMoleculeIterator - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
affectedMoleculeIterator - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
affectedMoleculeIterator - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
affectedMoleculeIterator - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
affectedMoleculeList - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
affectedMoleculeList - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
affectedMoleculeList - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
affectedMoleculeList - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
affectedMoleculeList - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
affectedMolecules(IBox) - Method in class etomica.association.MCMoveBiasUBMolecule
affectedMolecules(IBox) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
affectedMolecules(IBox) - Method in interface etomica.integrator.mcmove.MCMoveMolecular
affectedMolecules(IBox) - Method in class etomica.integrator.mcmove.MCMoveMolecule
affectedMolecules(IBox) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
affectedMolecules(IBox) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
affectedWV - Variable in class etomica.models.oneDHardRods.MeterWidomMode
affectedWV - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
affectedWV - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
ag - Variable in class etomica.meam.MEAM_MC
ag - Variable in class etomica.meam.MEAMMd3D
Ag - Static variable in class etomica.meam.ParameterSetMEAM
ag - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
Ag3Sn - Static variable in class etomica.meam.ParameterSetMEAM
agB - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
Agent() - Constructor for class etomica.association.MCMoveVolumeAssociated.Agent
Agent() - Constructor for class etomica.association.MCMoveVolumeAssociatedMolecule.Agent
Agent(ISpace) - Constructor for class etomica.integrator.IntegratorConNVT.Agent
Agent(ISpace) - Constructor for class etomica.integrator.IntegratorGear4.Agent
Agent(IAtom, IntegratorHard) - Constructor for class etomica.integrator.IntegratorHard.Agent
Agent(ISpace) - Constructor for class etomica.integrator.IntegratorVerlet.Agent
agentClass - Variable in class etomica.atom.AtomLeafAgentManager
AgentIterator(AtomLeafAgentManager<E>) - Constructor for class etomica.atom.AtomLeafAgentManager.AgentIterator
AgentIterator(AtomTypeAgentManager) - Constructor for class etomica.atom.AtomTypeAgentManager.AgentIterator
AgentIterator(MoleculeAgentManager) - Constructor for class etomica.atom.MoleculeAgentManager.AgentIterator
AgentIterator(SpeciesAgentManager) - Constructor for class etomica.atom.SpeciesAgentManager.AgentIterator
AgentIterator(BoxAgentManager<E>) - Constructor for class etomica.box.BoxAgentManager.AgentIterator
agentIterator - Variable in class etomica.potential.PotentialCalculationForceSum
agentManager - Variable in class etomica.atom.DiameterHashByType
agentManager - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
agentManager - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
agentManager - Variable in class etomica.graphics.ColorSchemeCollectiveAgent
agentManager - Variable in class etomica.integrator.IntegratorConNVT
agentManager - Variable in class etomica.integrator.IntegratorGear4
agentManager - Variable in class etomica.integrator.IntegratorHard
agentManager - Variable in class etomica.integrator.IntegratorVelocityVerlet
agentManager - Variable in class etomica.integrator.IntegratorVelocityVerletShake
agentManager - Variable in class etomica.integrator.IntegratorVerlet
agentManager - Variable in class etomica.interfacial.FixedWall
agentManager - Variable in class etomica.modules.catalysis.ColorSchemeRadical
agentManager - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
agentManager - Variable in class etomica.modules.catalysis.InteractionTracker
agentManager - Variable in class etomica.modules.catalysis.P2SquareWellBonding
agentManager - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
agentManager - Variable in class etomica.modules.catalysis.P2SquareWellSurface
agentManager - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
agentManager - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
agentManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
agentManager - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
agentManager - Variable in class etomica.modules.chainequilibrium.MeterChainLength
agentManager - Variable in class etomica.modules.chainequilibrium.MeterConversion
agentManager - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
agentManager - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
agentManager - Variable in class etomica.modules.droplet.AtomFilterLiquidAtomic
agentManager - Variable in class etomica.modules.droplet.IntegratorDroplet
agentManager - Variable in class etomica.modules.reactionequilibrium.MeterDimerFraction
agentManager - Variable in class etomica.modules.reactionequilibrium.P2SquareWellBonded
agentManager - Variable in class etomica.modules.rosmosis.MeterFlux
agentManager - Variable in class etomica.modules.rosmosis.P1Tether
agentManager - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
agentManager - Variable in class etomica.nbr.cell.NeighborCellManager
agentManager - Variable in class etomica.nbr.CriterionPositionWall
agentManager - Variable in class etomica.nbr.CriterionSimple
agentManager - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
agentManager - Variable in class etomica.normalmode.HSNPT.ActionSummer
agentManager - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
agentManager1Body - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
agentManager1Body - Variable in class etomica.nbr.list.NeighborListManager
agentManager2Body - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
agentManager2Body - Variable in class etomica.nbr.list.NeighborListManager
agents - Variable in class etomica.atom.AtomLeafAgentManager
agents - Variable in class etomica.atom.AtomTypeAgentManager
agents - Variable in class etomica.atom.MoleculeAgentManager
agents - Variable in class etomica.atom.SpeciesAgentManager
agents - Variable in class etomica.box.BoxAgentManager
agents - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
agents - Variable in class etomica.potential.P2SemiclassicalAtomic
agents - Variable in class etomica.potential.P2SemiclassicalMolecular
agentSource - Variable in class etomica.atom.AtomLeafAgentManager
agentSource - Variable in class etomica.atom.MoleculeAgentManager
agentSource - Variable in class etomica.box.BoxAgentManager
agFixedB - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
ahType - Variable in class etomica.models.rowley.SpeciesEthanol
ahType - Variable in class etomica.models.rowley.SpeciesMethanol
ai - Variable in class etomica.freeenergy.npath.SimIdealGas
ai - Variable in class etomica.freeenergy.npath.SimLJ
ai - Variable in class etomica.graphics.DeviceDelaySlider
ai - Variable in class etomica.interfacial.LJMC
ai - Variable in class etomica.interfacial.LJMD
ai - Variable in class etomica.liquidLJ.LjMC3D
ai - Variable in class etomica.liquidLJ.LjMd3D
ai - Variable in class etomica.modules.pistoncylinder.PistonCylinder
ai - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
ai - Variable in class etomica.normalmode.SimHSMDVacancy
ai - Variable in class etomica.normalmode.SimLJVacancy
Ai - Variable in class etomica.potential.PotentialCalculationPhiSum
ai - Variable in class etomica.rotation.DipoleBox
ai - Variable in class etomica.rotation.DipoleBoxMatrix
ai - Variable in class etomica.virial.simulations.SimulationVirial
ai - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
ai - Variable in class etomica.virial.simulations.SimulationVirialOverlap
ai - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
ai - Variable in class etomica.virial.simulations.SimulationVirialPT
aiInner - Variable in class etomica.atom.iterator.ApiInnerVariable: The iterators used to generate the sets of atoms.
aiInner - Variable in class etomica.atom.iterator.ApiIntergroup
aiInner - Variable in class etomica.atom.iterator.MpiInnerVariable: The iterators used to generate the sets of atoms.
aiInnerSize - Variable in class etomica.atom.iterator.ApiIntergroupExchange
aiOuter - Variable in class etomica.atom.iterator.ApiInnerVariable
aiOuter - Variable in class etomica.atom.iterator.ApiIntergroup
aiOuter - Variable in class etomica.atom.iterator.MpiInnerVariable
aiOuter - Variable in class etomica.atom.iterator.MpiIntraspecies1A
aiOuterSize - Variable in class etomica.atom.iterator.ApiIntergroupExchange
aj - Variable in class etomica.models.water.P2WaterSzalewicz
Aj - Variable in class etomica.potential.PotentialCalculationPhiSum
aj3 - Variable in class etomica.models.water.P2WaterSzalewicz
akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
akima - Variable in class etomica.overlap.DataOverlap
akima - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
akimaSpline - Variable in class etomica.models.nitrogen.FindTransitionTemperature
akimaSpline - Variable in class etomica.normalmode.SoftSphereSolidEOS
AkimaSpline - Class in etomica.util.numerical: DataProcessor that interpolates incoming data using an Akima spline interpolation scheme.
AkimaSpline() - Constructor for class etomica.util.numerical.AkimaSpline
AkimaSplineSmoother - Class in etomica.util.numerical: Optimization algorithm which attempts to smooth data without moving any point far from its original location.
AkimaSplineSmoother(IRandom) - Constructor for class etomica.util.numerical.AkimaSplineSmoother
AkimaSplineSmootherApp - Class in etomica.util.numerical: App to drive AkimaSplineSmoother
AkimaSplineSmootherApp(String) - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp
AkimaSplineSmootherApp.Applet - Class in etomica.util.numerical
AkimaSplineSmootherApp.IntegratorSmoother - Class in etomica.util.numerical
AkimaSplineSmootherApp.PlotAction - Class in etomica.util.numerical
AkimaSplineSmootherDy - Class in etomica.util.numerical: Optimization algorithm which attempts to smooth data without moving any point far from its original location.
AkimaSplineSmootherDy(IRandom) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDy
AkimaSplineSmootherDyApp - Class in etomica.util.numerical: App to drive AkimaSplineSmoother
AkimaSplineSmootherDyApp(String) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp
AkimaSplineSmootherDyApp.Applet - Class in etomica.util.numerical
AkimaSplineSmootherDyApp.IntegratorSmoother - Class in etomica.util.numerical
AkimaSplineSmootherDyApp.PlotAction - Class in etomica.util.numerical
AkimaSplineSmootherMain - Class in etomica.util.numerical: Main method to drive AkimaSplineSmoother
AkimaSplineSmootherMain() - Constructor for class etomica.util.numerical.AkimaSplineSmootherMain
AL10 - Static variable in class etomica.math.Gamma
al1l2l0(int, int, int, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
al1l2l0(int, int, int, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
alamda - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
alamda - Variable in class etomica.util.numerical.NonLinearCurveFitting
alarm - Class in etomica.mappedvirial
alarm() - Constructor for class etomica.mappedvirial.alarm
Alat - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
alfst - Static variable in class etomica.potential.P2WaterPotentialsJankowski
align - Variable in class etomica.graphics.DisplayBox
align - Variable in class etomica.graphics.DisplayPolytope
align_on_z_axis(IVectorMutable[], IVectorMutable[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
alignedV1 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
alignedV2 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
alkaneSpherePanel - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
all - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
ALL - Static variable in class etomica.units.Prefix
all - Static variable in class org.jmol.script.Token
allAtoms - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
allAtoms - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
allAtoms - Variable in class etomica.data.meter.MeterRDFPC
allatoms - Variable in class etomica.dimer.IntegratorDimerMin
allatoms - Variable in class etomica.dimer.IntegratorDimerRT
allAtoms - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
allAtoms - Variable in class etomica.integrator.IntegratorVelocityVerlet
allAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake
allAtoms - Variable in class etomica.mappedvirial.MappedUpotential
allAtoms - Variable in class etomica.mappedvirial.MeterMappedU
allAtoms - Variable in class etomica.mappedvirial.MeterMappedVirial
allAtoms - Variable in class etomica.mappedvirial.MeterMappedVirialV
allAtoms - Variable in class etomica.mappedvirial.MeterMeanForce
allAtoms - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
allAtoms - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
allAtoms - Variable in class etomica.modules.droplet.IntegratorDroplet
allAtoms - Variable in class etomica.surfacetension.SurfaceTensionMapped
allAtoms(IAtomList) - Static method in class etomica.util.Debug: determines if all of the atoms in the given array are set to be debugged (via ATOMx_NUM and setAtoms(box)).
allAtoms(IMoleculeList) - Static method in class etomica.util.Debug: determines if all of the atoms in the given array are set to be debugged (via ATOMx_NUM and setAtoms(box)).
allAtoms - Variable in class etomica.util.numerical.CalcGradientDifferentiable
allCriteria - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
allCriteria - Variable in class etomica.nbr.list.PotentialMasterList
AllData(long, IData, IData) - Constructor for class etomica.data.AccumulatorAverageBlockless.AllData
allData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
allData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
allDone() - Method in class etomica.modules.clustergenerator.MyApplet.Starter
allfloat - Static variable in class org.jmol.script.Token
AllIsomorphs - Class in etomica.graph.operations: Returns all graphs that are isomorphs of the original graph(s).
AllIsomorphs() - Constructor for class etomica.graph.operations.AllIsomorphs
AllIsomorphs.AllIsomorphsParameters - Class in etomica.graph.operations
AllIsomorphsParameters(boolean) - Constructor for class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
AllIsomorphsParameters(boolean, Property) - Constructor for class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
allLnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
allLnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
allMoleculeList - Variable in class etomica.box.Box
allMyData - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
allMyData - Variable in class etomica.virial.MeterVirialBinMultiThreaded
allMyData - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
allMyData - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
allMyData - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
allocateBitmap() - Method in class etomica.graph.model.impl.AbstractBitmap: Allocates the storage space for bitSize() bits.
allocateBitmap() - Method in class etomica.graph.model.impl.BitmapOfLong
allocateBitmap() - Method in class etomica.graph.model.impl.BitmapOfLongVector
allocateColix(int) - Static method in class org.jmol.util.Colix
allocateRgbImage(int, int, int[], int, boolean) - Method in interface org.jmol.api.ApiPlatform
allocateRgbImage(int, int, int[], int, boolean) - Method in class org.jmol.awt.Platform
allOr - Variable in class etomica.models.water.P2WaterSzalewicz
allOr0 - Variable in class etomica.models.co2.P2CO2H2OWheatley
allOr0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
allOr0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
allOr1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
allOr1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
allOr1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
ALLOWED - Static variable in class etomica.units.Prefix: Constant used when invoking constructor of SimpleUnit class to indicate that the unit permits the use of a prefix.
allowedQuaternionFrames - Static variable in class org.jmol.viewer.JmolConstants
allowedScriptTypes - Variable in class etomica.graph.view.rasterizer.SVGConverter: Set of allowed script types.
allowembeddedscripts - Static variable in class org.jmol.script.Token
allowgestures - Static variable in class org.jmol.script.Token
allowkeystrokes - Static variable in class org.jmol.script.Token
allowmodelkit - Static variable in class org.jmol.script.Token
allowmoveatoms - Static variable in class org.jmol.script.Token
allowmultitouch - Static variable in class org.jmol.script.Token
allowrotateselected - Static variable in class org.jmol.script.Token
allPermutations - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
allPermutations - Variable in class etomica.graph.operations.FactorOnce.FactorOnceParameters
allPermutations - Variable in class etomica.modules.clustergenerator.MyApplet
allPermutations - Variable in class etomica.virial.cluster.VirialDiagrams
allPermutations - Variable in class etomica.virial.cluster.VirialDiagramsMix2
allPermutations - Variable in class etomica.virial.cluster.VirialDiagramsPT
allPermutations - Variable in class etomica.virial.ClusterICPYC
allPermutationsCB - Variable in class etomica.modules.clustergenerator.MyApplet
allPotentials - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
allPotentials - Variable in class etomica.nbr.PotentialMasterNbr
allPotentials - Variable in class etomica.potential.PotentialMasterMonatomic
AllSigs(int) - Constructor for class etomica.virial.ClusterWheatleyHS.AllSigs
allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
allValueClusters - Variable in class etomica.virial.simulations.SimulationVirial
allValueClusters - Variable in class etomica.virial.simulations.SimulationVirialPT
allZero - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
alpha - Variable in class etomica.dimer.P1LepsHarmonic
alpha - Variable in class etomica.models.co2.P2CO2Hellmann
alpha - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
alpha - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
alpha - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
alpha - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
alpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
alpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
alpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
alpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
alpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
alpha - Variable in class etomica.modules.adsorption.EOSSWPatel
alpha - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
alpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
alpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
alpha - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
alpha - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
alpha - Variable in class etomica.normalmode.MCMoveHarmonicEin
alpha - Variable in class etomica.normalmode.MeterOverlapSwitch
alpha - Variable in class etomica.normalmode.MeterTargetTP
alpha - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
alpha - Variable in class etomica.overlap.MeterOverlap
alpha - Variable in class etomica.potential.EwaldSummation
alpha - Variable in class etomica.potential.EwaldSumMolecules
alpha - Static variable in class etomica.potential.P1HydrogenMielke
alpha - Static variable in class etomica.potential.P2HePCKLJS
alpha - Variable in class etomica.potential.P2NitrogenHellmann
alpha - Variable in class etomica.potential.P3AxilrodTeller.MyAgent
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHe
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
alpha - Variable in class etomica.potential.P3Induction
alpha - Variable in class etomica.potential.P3Induction.MyAgent
alpha - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
alpha - Variable in class etomica.util.numerical.NonLinearCurveFitting
alpha1 - Variable in class etomica.models.nitrogen.P2Nitrogen
alpha1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
alpha1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
alpha1 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
alpha2 - Variable in class etomica.models.nitrogen.P2Nitrogen
alpha2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
alpha2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
alpha2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
alpha2 - Variable in class etomica.potential.EwaldSummation
alpha3 - Variable in class etomica.potential.EwaldSummation
ALPHA_SHIFT - Static variable in class org.jmol.util.Colix
alphaA - Static variable in class etomica.models.co2.P2CO2Hellmann
alphaA - Static variable in class etomica.potential.P2NitrogenHellmann
alphaB - Static variable in class etomica.models.co2.P2CO2Hellmann
alphaB - Static variable in class etomica.potential.P2NitrogenHellmann
alphaCenter - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
alphaCenter - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
alphaCenter - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
alphaCenter - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
alphaCenter - Variable in class etomica.normalmode.MeterOverlapSwitch
alphaCenter - Variable in class etomica.normalmode.MeterTargetTP
alphaCenter - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
alphaCenter - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
alphaCenter - Variable in class etomica.overlap.MeterOverlap
alphaCenter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
alphaCenter - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
alphaChoice - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
alphaCoeffs - Variable in class etomica.models.nitrogen.FindTransitionTemperature
alphaData - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaFac - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
alphaInfo - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaIso - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
alphaIsoSim - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
alphaPar - Variable in class etomica.models.co2.PNCO2GCPM
alphaPar - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
alphaPerp - Variable in class etomica.models.co2.PNCO2GCPM
alphaPerp - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
alphaPol - Variable in class etomica.models.water.PNWaterGCPM
alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
AlphaSource - Interface in etomica.overlap: Class that can return values of alpha.
alphaSource - Variable in class etomica.overlap.DataOverlap
alphaSource - Variable in class etomica.virial.overlap.DataVirialOverlap
alphaSpan - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
alphaSpan - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
alphaSpan - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
alphaSpan - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
alphaSpan - Variable in class etomica.normalmode.MeterOverlapSwitch
alphaSpan - Variable in class etomica.normalmode.MeterTargetTP
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
alphaSpan - Variable in class etomica.overlap.MeterOverlap
alphaSpan - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
alphaSpan - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
alphaTag - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
alphaTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
alphaTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
ALPREC - Static variable in class etomica.math.Gamma
altArgbsCpk - Static variable in class org.jmol.viewer.JmolConstants
altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
altElementMax - Static variable in class org.jmol.util.Elements: length of the altElementSymbols, altElementNames, altElementNumbers arrays
altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
alternateStylesheet - Variable in class etomica.graph.view.rasterizer.SVGConverter: Alternate stylesheet for which should be applied to the SVG
altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
altloc - Static variable in class org.jmol.script.Token
altVertices - Variable in class org.jmol.util.MeshSurface
ambientFraction - Static variable in class org.jmol.util.Shader
ambientpercent - Static variable in class org.jmol.script.Token
ambientPercent - Static variable in class org.jmol.util.Shader
Ampere - Class in etomica.units: The ampere unit of electrical current.
AnalyticalDerivativeEnergyParacetamol - Class in etomica.paracetamol
AnalyticalDerivativeEnergyParacetamol(IBox, PotentialMaster, ISpace) - Constructor for class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
and(Bitmap) - Method in interface etomica.graph.model.Bitmap: and: bitmap -> bitmap = (bitmap & other).
and(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
and(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1) for a compatible instance of other.
and(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
and(BitSet) - Method in class org.jmol.util.BitSet: Performs a logical AND of this target bit set with the argument bit set.
ANDERSEN - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
ANDERSEN_SCALING - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
ANDERSEN_SINGLE - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
andNot(BitSet) - Method in class org.jmol.util.BitSet: Clears all of the bits in this BitSet whose corresponding bit is set in the specified BitSet.
andNot(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
angle - Variable in class etomica.lattice.crystal.Primitive
angle - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
angle - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
angle - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
angle - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
angle - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
angle - Variable in class etomica.potential.P3BondAngle
angle - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
angle - Variable in class etomica.space2d.Orientation2D
Angle - Class in etomica.units: Base for all angular units.
angle() - Method in class etomica.units.systems.CGS
angle() - Method in class etomica.units.systems.LJ
angle() - Method in class etomica.units.systems.MKS
angle() - Method in class etomica.units.systems.UnitSystem
angle() - Method in class etomica.units.systems.UnitSystem.Sim
angle - Static variable in class org.jmol.script.Token
angle - Variable in class org.jmol.util.AxisAngle4f: The angle.
angle(Vector3f) - Method in class org.jmol.util.Vector3f: Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
angleCCC - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
angleCCC - Variable in class etomica.virial.ConformationAlkaneEH
angleCCC_half - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
angleCCC_half - Variable in class etomica.virial.ConformationAlkaneEH
angleCCH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
angleCCH - Variable in class etomica.virial.ConformationAlkaneEH
angleHCH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
angleHCH - Variable in class etomica.virial.ConformationAlkaneEH
angleHCH_half - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
angleHCH_half - Variable in class etomica.virial.ConformationAlkaneEH
angleHOH - Static variable in class etomica.models.water.ConformationWater3P
angleHOH - Static variable in class etomica.models.water.ConformationWaterTIP4P
anglePanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
angles - Static variable in class etomica.potential.P2WaterPotentialsJankowski
Angstrom - Class in etomica.units
ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JmolConstants
angularMomentum - Variable in class etomica.atom.MoleculeOrientedDynamic
angularVelocity - Variable in class etomica.atom.AtomOrientedDynamic
angularVelocity - Variable in class etomica.data.meter.MeterKineticEnergyRigid
angularVelocity - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
animationfps - Static variable in class org.jmol.script.Token
ANIntergroupCoupled - Class in etomica.atom.iterator: Iterator that returns coupled iterates of any size; the first set contains the first atom from each basis.
ANIntergroupCoupled(int) - Constructor for class etomica.atom.iterator.ANIntergroupCoupled
ANIntergroupExchange - Class in etomica.atom.iterator
ANIntergroupExchange(int) - Constructor for class etomica.atom.iterator.ANIntergroupExchange
anIntragroupExchange - Variable in class etomica.atom.iterator.ANIntergroupExchange
ANIntragroupExchange - Class in etomica.atom.iterator
ANIntragroupExchange(int, int) - Constructor for class etomica.atom.iterator.ANIntragroupExchange
anoise - Static variable in class etomica.potential.P2WaterPotentialsJankowski
antialiasdisplay - Static variable in class org.jmol.script.Token
antialiasEnabled - Variable in class org.jmol.util.GData
antialiasimages - Static variable in class org.jmol.script.Token
antialiasThisFrame - Variable in class org.jmol.util.GData
antialiastranslucent - Static variable in class org.jmol.script.Token
aNumber - Variable in class etomica.modules.materialfracture.MeterElongation
aNumber - Variable in class etomica.modules.materialfracture.MeterStrain
anx - Static variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
anyAtom(IAtomList) - Static method in class etomica.util.Debug: determines whether any of the atoms in the given array are set to be debugged (via ATOMx_NUM)
anyMolecule(IMoleculeList) - Static method in class etomica.util.Debug: determines whether any of the atoms in the given array are set to be debugged (via ATOMx_NUM)
aPair - Variable in class etomica.virial.MayerGeneralAtomic
aPairSet - Variable in class etomica.virial.BoxCluster
api - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
Api1ACell - Class in etomica.nbr.cell: Generates pairs that are cell-based neighbors of a specific Atom.
Api1ACell(int, double, BoxAgentManager) - Constructor for class etomica.nbr.cell.Api1ACell: Constructor makes iterator that must have box specified and then be reset() before iteration.
Api1ASite - Class in etomica.nbr.site: Iteration is performed using site lists.
Api1ASite(int, BoxAgentManager) - Constructor for class etomica.nbr.site.Api1ASite: Constructor makes iterator that must have box specified and then be reset() before iteration.
ApiAACell - Class in etomica.nbr.cell: Returns iterates formed from all cell-based neighbor pairs.
ApiAACell(int, double, IBox) - Constructor for class etomica.nbr.cell.ApiAACell: Constructor makes iterator that must have box specified and then be reset() before iteration.
ApiBuilder - Class in etomica.atom.iterator: Provides static methods for construction of some useful pair iterators.
apiDown - Variable in class etomica.atom.iterator.MpiIntraspecies1A
ApiFilteredCylinder - Class in etomica.modules.pistoncylinder: Our own ApiFiltered that's box-dependent
ApiFilteredCylinder(ApiFilteredCylinder.AtomFilterInCylinder) - Constructor for class etomica.modules.pistoncylinder.ApiFilteredCylinder
ApiFilteredCylinder.AtomFilterInCylinder - Class in etomica.modules.pistoncylinder: Filter to expclude any pair with an atom within some distance from a wall.
ApiIndexList - Class in etomica.atom.iterator: Iterator that returns intramolecular pairs of atoms with specific indices.
ApiIndexList(int[][]) - Constructor for class etomica.atom.iterator.ApiIndexList: Constructs iterator without defining atoms in pair.
ApiInnerVariable - Class in etomica.atom.iterator: Pair iterator synthesized from two atom iterators, such that the inner-loop iteration depends on the outer-loop atom.
ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiInnerVariable: Construct a pair iterator using the given atom iterators.
ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent, boolean) - Constructor for class etomica.atom.iterator.ApiInnerVariable: Construct a pair iterator using the given atom iterators, indicating whether the atoms ordering in the AtomPair should be swapped from the default behavior.
ApiInterArrayList - Class in etomica.atom.iterator: Returns all pairs formed from two different untabbed lists of atoms.
ApiInterArrayList() - Constructor for class etomica.atom.iterator.ApiInterArrayList: Construct iterator with an empty lists.
ApiInterArrayList(IAtomList, IAtomList) - Constructor for class etomica.atom.iterator.ApiInterArrayList: Constructs iterator to return pairs from the given lists.
ApiIntergroup - Class in etomica.atom.iterator: Iterator that returns pairs formed using two different basis atoms, so that the iterates are taken from two different groups.
ApiIntergroup() - Constructor for class etomica.atom.iterator.ApiIntergroup: Default iterator is an ApiInnerFixed formed from two AtomIteratorBasis instances.
ApiIntergroup(AtomIteratorBasisDependent, AtomIteratorBasisDependent) - Constructor for class etomica.atom.iterator.ApiIntergroup: Constructs a pair iterator that returns iterates from the given pairIterator, which is expected to contain two basis-dependent iterators.
ApiIntergroupCoupled - Class in etomica.atom.iterator: Iterator that returns coupled iterates; the first pair contains the first atom from each basis.
ApiIntergroupCoupled() - Constructor for class etomica.atom.iterator.ApiIntergroupCoupled
ApiIntergroupCoupled(AtomIteratorBasis, AtomIteratorBasis) - Constructor for class etomica.atom.iterator.ApiIntergroupCoupled
ApiIntergroupExchange - Class in etomica.atom.iterator
ApiIntergroupExchange(int) - Constructor for class etomica.atom.iterator.ApiIntergroupExchange
ApiIntergroupIntraSpecies - Class in etomica.atom.iterator: Iterator that returns pairs formed using two different basis atoms, so that the iterates are taken from two different groups.
ApiIntergroupIntraSpecies(AtomIteratorBasisDependent, AtomIteratorBasisDependent) - Constructor for class etomica.atom.iterator.ApiIntergroupIntraSpecies: Constructs a pair iterator that returns iterates from the given pairIterator, which is expected to contain two basis-dependent iterators.
ApiIntraArrayList - Class in etomica.atom.iterator: Returns all pairs formed from a single list of atoms.
ApiIntraArrayList() - Constructor for class etomica.atom.iterator.ApiIntraArrayList: Construct iterator with an empty list.
ApiIntraArrayList(IAtomList) - Constructor for class etomica.atom.iterator.ApiIntraArrayList: Constructs iterator to return pairs from the given list.
ApiIntragroup - Class in etomica.atom.iterator: Returns iterates from the childList of a single basis atom.
ApiIntragroup() - Constructor for class etomica.atom.iterator.ApiIntragroup: Constructor makes iterator that must have basis specified and then be reset() before iteration.
ApiIntragroup(AtomIteratorAtomDependent, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiIntragroup
ApiIntragroup(AtomsetIteratorBasisDependent, AtomIteratorAtomDependent, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiIntragroup
ApiLeafAtoms - Class in etomica.atom.iterator: Iterator that returns all pairs that can be formed from all leaf atoms of a given box.
ApiLeafAtoms() - Constructor for class etomica.atom.iterator.ApiLeafAtoms: Creates new pair iterator that requires reset() before beginning iteration.
ApiPlatform - Interface in org.jmol.api
apiPlatform - Variable in class org.jmol.util.GData
APIPotentialReference(MeterHarmonicEnergy[]) - Constructor for class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
APIPotentialTarget(IPotentialMaster) - Constructor for class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
apiUp - Variable in class etomica.atom.iterator.MpiIntraspecies1A
APP_NAME - Static variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
AppControllerMixtureBuilder - Class in etomica.virial.GUI.controllers
AppControllerMixtureBuilder(AppViewMixtureBuilder, AppModelMixtureBuilder) - Constructor for class etomica.virial.GUI.controllers.AppControllerMixtureBuilder
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialCO2PI
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialCO2PI
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PI
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PI
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePI
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePI
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXC
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXC
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
append(String) - Method in class org.jmol.util.StringXBuilder
appendB(boolean) - Method in class org.jmol.util.StringXBuilder
appendC(char) - Method in class org.jmol.util.StringXBuilder
appendCB(char[], int, int) - Method in class org.jmol.util.StringXBuilder
appendD(double) - Method in class org.jmol.util.StringXBuilder
appendF(float) - Method in class org.jmol.util.StringXBuilder: note that JavaScript could drop off the ".0" in "1.0"
appendI(int) - Method in class org.jmol.util.StringXBuilder
appendnew - Static variable in class org.jmol.script.Token
appendO(Object) - Method in class org.jmol.util.StringXBuilder
appendSB(StringXBuilder) - Method in class org.jmol.util.StringXBuilder
AppFrameMixtureBuilder - Class in etomica.virial.GUI.containers
AppFrameMixtureBuilder(String) - Constructor for class etomica.virial.GUI.containers.AppFrameMixtureBuilder
Applet() - Constructor for class etomica.graphics.DisplayPolytope.Applet
Applet() - Constructor for class etomica.modules.adsorption.AdsorptionGraphic.Applet
Applet() - Constructor for class etomica.modules.catalysis.CatalysisGraphic.Applet
Applet() - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet
Applet() - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet
Applet() - Constructor for class etomica.modules.colloid.ColloidGraphic.Applet
Applet() - Constructor for class etomica.modules.crystalviewer.CrystalViewer.Applet
Applet() - Constructor for class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet
Applet() - Constructor for class etomica.modules.droplet.DropletAtomicGraphic.Applet
Applet() - Constructor for class etomica.modules.droplet.DropletGraphic.Applet
Applet() - Constructor for class etomica.modules.ensembles.LJMCGraphic.Applet
Applet() - Constructor for class etomica.modules.entropylottery.EntropyLotteryGraphic.Applet
Applet() - Constructor for class etomica.modules.insertion.InsertionGraphic.Applet
Applet() - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.Applet
Applet() - Constructor for class etomica.modules.joulethomson.JouleThomson.Applet
Applet() - Constructor for class etomica.modules.ljmd.LjmdGraphic.Applet
Applet() - Constructor for class etomica.modules.materialfracture.MaterialFractureGraphic.Applet
Applet() - Constructor for class etomica.modules.mu.MuGraphic.Applet
Applet() - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet
Applet() - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet
Applet() - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet
Applet() - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet
Applet() - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet
Applet() - Constructor for class etomica.modules.osmosis.Osmosis.Applet
Applet() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet
Applet() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet
Applet() - Constructor for class etomica.modules.rheology.RheologyGraphic.Applet
Applet() - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet
Applet() - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet
Applet() - Constructor for class etomica.modules.sam.SamGraphic.Applet
Applet() - Constructor for class etomica.modules.swmd.SwmdGraphic.Applet
Applet() - Constructor for class etomica.modules.vle.B2Fit.Applet
Applet() - Constructor for class etomica.modules.vle.VLE.Applet
Applet() - Constructor for class etomica.normalmode.HTTPSoftSphereApplet.Applet
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1D.Applet
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3D.Applet
Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet
Applet() - Constructor for class etomica.normalmode.nptdemo.HSNPT2DGraphic.Applet
Applet() - Constructor for class etomica.normalmode.SimLJVacancy.Applet
Applet() - Constructor for class etomica.rotation.DipoleBox.Applet
Applet() - Constructor for class etomica.rotation.DipoleBoxMatrix.Applet
Applet() - Constructor for class etomica.rotation.SingleDipole.Applet
Applet() - Constructor for class etomica.rotation.SingleDumbellRattle.Applet
Applet() - Constructor for class etomica.rotation.SingleDumbellShake.Applet
Applet() - Constructor for class etomica.rotation.SingleWater.Applet
Applet() - Constructor for class etomica.rotation.SingleWaterMatrix.Applet
Applet() - Constructor for class etomica.rotation.SingleWaterRattle.Applet
Applet() - Constructor for class etomica.rotation.SingleWaterShake.Applet
Applet() - Constructor for class etomica.rotation.WaterBox.Applet
Applet() - Constructor for class etomica.rotation.WaterDroplet.Applet
Applet() - Constructor for class etomica.rotation.WaterDropletMatrix.Applet
Applet() - Constructor for class etomica.rotation.WaterDropletRattle.Applet
Applet() - Constructor for class etomica.rotation.WaterDropletShake.Applet
Applet() - Constructor for class etomica.rotation.WaterTrimer.Applet
Applet() - Constructor for class etomica.rotation.WaterTrimerRattle.Applet
Applet() - Constructor for class etomica.rotation.WaterTrimerShake.Applet
Applet() - Constructor for class etomica.simulation.prototypes.LjMd3D.Applet
Applet() - Constructor for class etomica.thermointegration.LjMc3D.Applet
Applet() - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp.Applet
Applet() - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp.Applet
appletproxy - Static variable in class org.jmol.script.Token
ApplicationMixtureBuilder - Class in etomica.virial.GUI
ApplicationMixtureBuilder() - Constructor for class etomica.virial.GUI.ApplicationMixtureBuilder
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.AllIsomorphs
apply(Graph, AllIsomorphs.AllIsomorphsParameters) - Method in class etomica.graph.operations.AllIsomorphs
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.BiComponentSubst
apply(Graph, BiComponentSubst.BiComponentSubstParameters) - Method in class etomica.graph.operations.BiComponentSubst
apply(Set<Graph>, Set<Graph>, Parameters) - Method in interface etomica.graph.operations.Binary
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.CombineABSite
apply(Graph, CombineABSite.CombineABSiteParameters) - Method in class etomica.graph.operations.CombineABSite
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.ComponentSubst
apply(Graph, ComponentSubst.ComponentSubstParameters) - Method in class etomica.graph.operations.ComponentSubst
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Conv
apply(Graph, Graph, ConvParameters) - Method in class etomica.graph.operations.Conv
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Decorate
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheim2Site
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheim2SiteRho
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheim3SiteRho
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Delete
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DeleteEdge
apply(Graph, DeleteEdgeParameters) - Method in class etomica.graph.operations.DeleteEdge
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DifByConstant
apply(Graph, DifByConstant.DifByConstantParameters) - Method in class etomica.graph.operations.DifByConstant
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DifByEdge
apply(Graph, DifParameters) - Method in class etomica.graph.operations.DifByEdge
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DifByNode
apply(Graph) - Method in class etomica.graph.operations.DropOrphanNodes
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Exclude
apply(Graph, ExcludeParameters) - Method in class etomica.graph.operations.Exclude
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Exp
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Factor
apply(Graph, MulFlexible.MulFlexibleParameters) - Method in class etomica.graph.operations.Factor
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.FactorOnce
apply(Graph, FactorOnce.FactorOnceParameters) - Method in class etomica.graph.operations.FactorOnce
apply(Graph, List<Integer>, List<Integer>) - Method in class etomica.graph.operations.FactorOnce
apply(Graph, List<Byte>) - Method in class etomica.graph.operations.GraphExtract
apply(Graph) - Method in interface etomica.graph.operations.GraphOp
apply(Graph) - Method in class etomica.graph.operations.GraphOp.GraphOpNull
apply(Graph) - Method in class etomica.graph.operations.GraphOpMaxRoot
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.IdenticalFree
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Int
apply(Graph, IntParameters) - Method in class etomica.graph.operations.Int
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.IsoFree
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.MaxIsomorph
apply(Graph, MaxIsomorph.MaxIsomorphParameters) - Method in class etomica.graph.operations.MaxIsomorph
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.MaxIsomorphWertheim
apply(Graph, MaxIsomorphWertheim.MaxIsomorphWertheimParameters) - Method in class etomica.graph.operations.MaxIsomorphWertheim
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Mul
apply(Graph, Graph, Mul.MulParameters) - Method in class etomica.graph.operations.Mul
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.MulFlexible
apply(Set<Graph>, Set<Graph>[], Parameters) - Method in class etomica.graph.operations.MulFlexible
apply(Graph, Graph, MulFlexible.MulFlexibleParameters) - Method in class etomica.graph.operations.MulFlexible
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.MulScalar
apply(Graph, MulScalarParameters) - Method in class etomica.graph.operations.MulScalar
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.MulUnion
apply(Graph, Graph) - Method in class etomica.graph.operations.MulUnion
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.NCopy
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.PCopy
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Pow
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.ReeHoover
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Relabel
apply(Graph, RelabelParameters) - Method in class etomica.graph.operations.Relabel
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.RelabelWertheim
apply(Graph, RelabelParameters) - Method in class etomica.graph.operations.RelabelWertheim
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.SetPropertyFilter
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Split
apply(Graph, SplitParameters) - Method in class etomica.graph.operations.Split
apply(Graph) - Method in class etomica.graph.operations.SplitGraph
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.SplitOne
apply(Graph, SplitOne.SplitOneParameters) - Method in class etomica.graph.operations.SplitOne
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.SplitOneBiconnected
apply(Graph, SplitOneBiconnected.SplitOneParametersBC) - Method in class etomica.graph.operations.SplitOneBiconnected
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Sub
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Sum
apply(Set<Graph>, Parameters) - Method in interface etomica.graph.operations.Unary
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.UnaryChain
apply(Graph, MulScalarParameters) - Method in class etomica.graph.operations.UnaryChain
apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Unfactor
apply(Graph, MulFlexible.MulFlexibleParameters) - Method in class etomica.graph.operations.Unfactor
apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Union
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitution
apply(Graph, BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site) - Method in class etomica.virial.cluster.BondConnectedSubstitution
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitution3Site
apply(Graph, BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site) - Method in class etomica.virial.cluster.BondConnectedSubstitution3Site
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
apply(Graph, BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa) - Method in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.CondenseExchange
apply(Graph, CondenseExchange.CondenseExchangeParameters) - Method in class etomica.virial.cluster.CondenseExchange
apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.ExchangeSplit
applyAnaglygh(EnumStereoMode, int[]) - Method in class org.jmol.g3d.Graphics3D
applyAnaglygh(EnumStereoMode, int[]) - Method in class org.jmol.util.GData
applyBlueAnaglyph() - Method in class org.jmol.g3d.Graphics3D
applyColorTranslucencyLevel(short, float) - Static method in class org.jmol.util.Colix
applyCustomAnaglyph(int[]) - Method in class org.jmol.g3d.Graphics3D
applyCyanAnaglyph() - Method in class org.jmol.g3d.Graphics3D
applyExponentPattern(String) - Method in class etomica.util.ScientificFormat
applyGreenAnaglyph() - Method in class org.jmol.g3d.Graphics3D
applyLocalizedPattern(String) - Method in class etomica.util.ScientificFormat
applyMantissaPattern(String) - Method in class etomica.util.ScientificFormat
applyPattern(String) - Method in class etomica.util.ScientificFormat: apply this pattern
applysymmetrytobonds - Static variable in class org.jmol.script.Token
applyTranslationRotation() - Method in class etomica.math.geometry.Polytope: Calculate transformed vertices from current values of vertices, position, and orientation.
AppModelMixtureBuilder - Class in etomica.virial.GUI.models
AppModelMixtureBuilder() - Constructor for class etomica.virial.GUI.models.AppModelMixtureBuilder
appName - Variable in class etomica.graphics.SimulationGraphic
approx(float, float) - Static method in class org.jmol.util.Parser
AppViewMixtureBuilder - Class in etomica.virial.GUI.views
AppViewMixtureBuilder(AppFrameMixtureBuilder, AppModelMixtureBuilder) - Constructor for class etomica.virial.GUI.views.AppViewMixtureBuilder
aProj - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
area - Variable in class etomica.graph.view.rasterizer.SVGConverter: Output AOI area.
Area - Class in etomica.units: Base for all area units.
area() - Method in class etomica.units.systems.CGS
area() - Method in class etomica.units.systems.LJ
area() - Method in class etomica.units.systems.MKS
area() - Method in class etomica.units.systems.UnitSystem
area() - Method in class etomica.units.systems.UnitSystem.Sim
areBonded(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: This function tells you if two atoms are bonded This could probably be public, although a public version would need to first re-retrieve agents
areBonded(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: This function tells you if two atoms are bonded
areEqual(ScriptVariable, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
areEqual(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
aRef - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
aRef - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
aRef - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
aRef - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
arep - Variable in class etomica.potential.P2HydrogenHinde
arep - Variable in class etomica.potential.P2HydrogenHindeAtomic
aResidualFcc(double, double) - Static method in class etomica.statmech.LennardJones: Molar Helmholtz free energy for the fcc solid, in excess of an ideal gas at the same temperature and density.
arg() - Method in class etomica.math.Complex: Argument of this Complex number, the angle in radians with the x-axis in polar coordinates.
argbCurrent - Variable in class org.jmol.util.GData
argbsAmino - Static variable in class org.jmol.viewer.JmolConstants
argbsChainAtom - Static variable in class org.jmol.viewer.JmolConstants: some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
argbsChainHetero - Static variable in class org.jmol.viewer.JmolConstants
argbsCpk - Static variable in enum org.jmol.constant.EnumPalette: Default table of CPK atom colors.
argbsCpkRasmol - Static variable in enum org.jmol.constant.EnumPalette
argbsFormalCharge - Static variable in class org.jmol.viewer.JmolConstants
argbShapelyBackbone - Static variable in class org.jmol.viewer.JmolConstants
argbShapelyDefault - Static variable in class org.jmol.viewer.JmolConstants
argbShapelySpecial - Static variable in class org.jmol.viewer.JmolConstants
argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JmolConstants
argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JmolConstants
argbsRoygbScale - Static variable in class org.jmol.viewer.JmolConstants
argbsRwbScale - Static variable in class org.jmol.viewer.JmolConstants
argbsShapely - Static variable in class org.jmol.viewer.JmolConstants
Argon - Class in etomica.chem.elements: Class for the Argon element.
Argon(String) - Constructor for class etomica.chem.elements.Argon
Argon(String, double) - Constructor for class etomica.chem.elements.Argon
args - Variable in class etomica.graph.view.rasterizer.Main: List of arguments describing the conversion task to be performed.
array - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
array - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
array - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
array - Static variable in class org.jmol.script.Token
ArrayA2B - Class in etomica.normalmode: Reads a file containing n mxm matrices as ASCII and serializes them to another file.
ArrayA2B() - Constructor for class etomica.normalmode.ArrayA2B
ArrayB2A - Class in etomica.normalmode: Reads a file containing n mxm matrices as (serialized) binary data and writes them to another file as text (ASCII).
ArrayB2A() - Constructor for class etomica.normalmode.ArrayB2A
arrayCollect(String[], String[]) - Static method in class etomica.util.Strings: Takes the elements of two string arrays and collects them into a new array containing both sets of strings.
arrayCopyBool(boolean[], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyByte(byte[], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyF(float[], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyI(int[], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyII(int[][], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyObject(Object, int) - Static method in class org.jmol.util.ArrayUtil: note -- cannot copy if array is null!
arrayCopyPt(Point3f[], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyRangeI(int[], int, int) - Static method in class org.jmol.util.ArrayUtil: a specialized method that allows copying from a starting point either to the end or to the middle (color schemes, especially)
arrayCopyRangeRevI(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyS(String[], int) - Static method in class org.jmol.util.ArrayUtil
arrayCopyShort(short[], int) - Static method in class org.jmol.util.ArrayUtil
arrayIndex(int[]) - Method in class etomica.lattice.RectangularLattice: Returns the index in the 1-d array for the site corresponding to the given lattice index.
ArrayMoleculeDisplayList - Class in etomica.virial.GUI.components
ArrayMoleculeDisplayList() - Constructor for class etomica.virial.GUI.components.ArrayMoleculeDisplayList
ArrayReader1D - Class in etomica.normalmode: Reads in lots of 1D arrays from a file.
ArrayReader1D() - Constructor for class etomica.normalmode.ArrayReader1D
ArrayReader1D - Class in etomica.util.numerical: Reads in lots of 1D arrays from a file.
ArrayReader1D() - Constructor for class etomica.util.numerical.ArrayReader1D
ArrayReader2D - Class in etomica.normalmode: Reads in lots of 2D arrays from a file.
ArrayReader2D() - Constructor for class etomica.normalmode.ArrayReader2D
Arrays - Class in etomica.util: Non-instantiable class with static utility methods for working with arrays.
arrayShape - Variable in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
arrayShape - Variable in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
ArrayUtil - Class in org.jmol.util
ArrayUtil() - Constructor for class org.jmol.util.ArrayUtil
ArticulatedAt0(boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
ArticulatedAt0(boolean, char) - Constructor for class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
ArticulatedAt0(boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
ArticulatedAt0(boolean, char) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
articulationPair - Variable in class etomica.graph.property.FFTDecomposition
articulationPoints - Variable in class etomica.graph.property.HasSimpleArticulationPoint
asBoolean() - Method in class org.jmol.script.ScriptVariable
asFloat() - Method in class org.jmol.script.ScriptVariable
asin(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The inverse trigonometric sine.
asinh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The inverse hyperbolic sine.
asInt() - Method in class org.jmol.script.ScriptVariable
Asolid(double) - Static method in class etomica.statmech.HardSphereFluid: Returns the difference between absolute free energies between the given densities for solid (FCC) hard spheres.
Asolid(double, int) - Static method in class etomica.statmech.HardSphereFluid
Asolid(double) - Static method in class etomica.statmech.HardSphereSolid: Returns the difference between absolute free energies between the given densities for solid (FCC) hard spheres.
Asolid(double, int) - Static method in class etomica.statmech.HardSphereSolid
aspectRatio - Variable in class etomica.surfacetension.LJMC.LJMCParams
assignCell(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Assigns the cell for the given atom.
assignCell(IAtom) - Method in class etomica.nbr.cell.NeighborCellManager: Assigns the cell for the given atom.
assignCellAll() - Method in interface etomica.box.BoxCellManager: Assigns cells to all molecules in the box.
assignCellAll() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Assigns cells to all interacting atoms in the box.
assignCellAll() - Method in class etomica.nbr.cell.NeighborCellManager: Assigns cells to all interacting atoms in the box.
assignCellAll() - Method in class etomica.nbr.site.NeighborSiteManager: Should not be called, because cell assignments are made as atoms are created.
assignColumnFrom(int, double[]) - Method in class etomica.data.types.DataDoubleArray: Assigns values in given array to the i-th "hypercolumn" of this data array.
assignColumnFrom(int, BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray: Assigns values in given array to the i-th "hypercolumn" of this data array.
assignColumnTo(int, double[]) - Method in class etomica.data.types.DataDoubleArray: Assigns values in the i=th "hypercolumn" of this array to the given array.
assignColumnTo(int, BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray: Assigns values in the i=th "hypercolumn" of this array to the given array.
AssignmentImpl - Class in etomica.graph.engine.impl
AssignmentImpl(Parser.Variable, Parser.StrictExpression) - Constructor for class etomica.graph.engine.impl.AssignmentImpl
assignSubsectionFrom(int[], double[]) - Method in class etomica.data.types.DataDoubleArray: Assigns values in the given array to the subsection of this array beginning at the specified index.
assignSubsectionFrom(int[], double[]) - Method in class etomica.data.types.DataDoubleBDArray: Assigns values in the given array to the subsection of this array beginning at the specified index.
assignTo(double[]) - Method in interface etomica.api.IVector: Assigns the components of this vector to the elements of the given array.
assignTo(double[]) - Method in interface etomica.data.IData: Fills the given array with the values held by this Data instance.
assignTo(double[]) - Method in class etomica.data.types.DataDouble: Returns a new one-element array formed from the current value of this instance.
assignTo(double[]) - Method in class etomica.data.types.DataDoubleArray: Returns the encapsulated array, implementing the Data interface.
assignTo(double[]) - Method in class etomica.data.types.DataDoubleBDArray: Returns the encapsulated array, implementing the Data interface.
assignTo(double[]) - Method in class etomica.data.types.DataGroup
assignTo(double[]) - Method in class etomica.data.types.DataTable: Returns a new array formed from the values held by the data instance.
assignTo(double[]) - Method in class etomica.data.types.DataTensor: Returns a new array formed by the elements of the wrapped tensor.
assignTo(double[]) - Method in class etomica.data.types.DataVector: Assigns the elements of the wrapped vector to the given array.
assignTo(IVectorMutable[]) - Method in interface etomica.space.Tensor: Assigns the tensor elements column-wise to the given vectors.
assignTo(double[]) - Method in interface etomica.space.Tensor: Fills the given array with the elements of this tensor.
assignTo(double[][]) - Method in interface etomica.space.Tensor
assignTo(IVectorMutable[]) - Method in class etomica.space1d.Tensor1D
assignTo(double[]) - Method in class etomica.space1d.Tensor1D
assignTo(double[][]) - Method in class etomica.space1d.Tensor1D
assignTo(double[]) - Method in class etomica.space1d.Vector1D
assignTo(IVectorMutable[]) - Method in class etomica.space2d.Tensor2D
assignTo(double[]) - Method in class etomica.space2d.Tensor2D
assignTo(double[][]) - Method in class etomica.space2d.Tensor2D
assignTo(double[]) - Method in class etomica.space2d.Vector2D
assignTo(IVectorMutable[]) - Method in class etomica.space3d.Tensor3D
assignTo(double[]) - Method in class etomica.space3d.Tensor3D
assignTo(double[][]) - Method in class etomica.space3d.Tensor3D
assignTo(double[]) - Method in class etomica.space3d.Vector3D
assignTo(IVectorMutable[]) - Method in class etomica.spaceNd.TensorND
assignTo(double[]) - Method in class etomica.spaceNd.TensorND
assignTo(double[][]) - Method in class etomica.spaceNd.TensorND
assignTo(double[]) - Method in class etomica.spaceNd.VectorND
assignToBasket(int, int[]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets: Allows the user to choose which wavevectors are in which basket.
AssociatedPolynomial - Class in etomica.util
AssociatedPolynomial() - Constructor for class etomica.util.AssociatedPolynomial
association(MayerFunction, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterAceticAcid
association(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
association(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
association(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
association2(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
association2(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
association2(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
association3(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
association3(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
association3(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
association4(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
association4(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
association4(MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
association5(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
association5(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
association6(MoleculePair, MoleculePair, IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
AssociationDefinition - Interface in etomica.association: Interface for a method that defines whether two atoms are considered associated.
AssociationDefinitionMolecule - Interface in etomica.association: Interface for a method that defines whether two molecules are considered associated.
associationEnergy - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
associationHelper - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
associationHelper - Variable in class etomica.association.ColorSchemeSmer
associationHelper - Variable in class etomica.association.ColorSchemeSmerByLength
associationHelper - Variable in class etomica.association.MCMoveMoleculeMonomer
associationHelper - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
associationHelper - Variable in class etomica.association.MCMoveMoleculeSmer
associationHelper - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
associationHelper - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
associationHelper - Variable in class etomica.association.TestLJAssociationMC3D_NPT
associationHelper - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
associationHelper - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
AssociationHelperBranched - Class in etomica.association: AssociationHelperBranched is capable of populating a list of atoms in an smer within a simulation with multiple association sites per atom.
AssociationHelperBranched(ISpace, IBox, AssociationManager) - Constructor for class etomica.association.AssociationHelperBranched
AssociationHelperDouble - Class in etomica.association: AssociationHelperDouble is capable of populating a list of atoms in an smer within a simulation with double-bonding (two bonding sites per atom).
AssociationHelperDouble(ISpace, IBox, AssociationManager) - Constructor for class etomica.association.AssociationHelperDouble
AssociationHelperMolecule - Class in etomica.association: AssociationHelperBranched is capable of populating a list of molecules in an smer within a simulation with multiple association sites per molecule.
AssociationHelperMolecule(ISpace, IBox, AssociationManagerMolecule) - Constructor for class etomica.association.AssociationHelperMolecule
AssociationHelperSingle - Class in etomica.association: AssociationHelperSingle is capable of populating a list of atoms in an smer within a simulation with single-bonding (one bonding site per atom).
AssociationHelperSingle(AssociationManager) - Constructor for class etomica.association.AssociationHelperSingle
associationManager - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
associationManager - Variable in class etomica.association.AssociationHelperBranched
associationManager - Variable in class etomica.association.AssociationHelperDouble
associationManager - Variable in class etomica.association.AssociationHelperMolecule
associationManager - Variable in class etomica.association.AssociationHelperSingle
AssociationManager - Class in etomica.association: Class to define and track atom associations.
AssociationManager(IBox, PotentialMasterCell, AssociationDefinition) - Constructor for class etomica.association.AssociationManager
associationManager - Variable in class etomica.association.AtomSourceRandomDimer
associationManager - Variable in class etomica.association.AtomSourceRandomMonomer
associationManager - Variable in class etomica.association.AtomSourceRandomSmer
associationManager - Variable in class etomica.association.MCMoveAtomDimer
associationManager - Variable in class etomica.association.MCMoveAtomMonomer
associationManager - Variable in class etomica.association.MCMoveAtomNoSmer
associationManager - Variable in class etomica.association.MCMoveAtomSmer
associationManager - Variable in class etomica.association.MCMoveDimer
associationManager - Variable in class etomica.association.MCMoveDimerRotate
associationManager - Variable in class etomica.association.MCMoveMoleculeMonomer
associationManager - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
associationManager - Variable in class etomica.association.MCMoveMoleculeSmer
associationManager - Variable in class etomica.association.MCMoveRotateAssociated
associationManager - Variable in class etomica.association.MCMoveRotateNoSmer
associationManager - Variable in class etomica.association.MCMoveSmer
associationManager - Variable in class etomica.association.MCMoveSmerRotate
associationManager - Variable in class etomica.association.MCMoveVolumeAssociated
associationManager - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
associationManager - Variable in class etomica.association.MoleculeSourceRandomDimer
associationManager - Variable in class etomica.association.MoleculeSourceRandomMonomer
AssociationManagerMolecule - Class in etomica.association: Class to define and track molecule associations.
AssociationManagerMolecule(ISimulation, IBox, BoxAgentManager<NeighborCellManagerMolecular>, AssociationDefinitionMolecule, double) - Constructor for class etomica.association.AssociationManagerMolecule
associationManagerOriented - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
associationManagerOriented - Variable in class etomica.association.TestLJAssociationMC3D_NPT
associationManagerOriented - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
associationManagerOriented - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
asString() - Method in class org.jmol.script.ScriptVariable
asymp(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
asymp(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
at(int) - Method in class etomica.veos.bigdecimal.Bernoulli: The Bernoulli number at the index provided.
at(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Retrieve a polynomial coefficient.
at(int) - Method in class etomica.veos.bigdecimal.Euler: The Euler number at the index provided.
at(int) - Method in class etomica.veos.bigdecimal.EulerPhi: Compute phi(n).
at(BigInteger) - Method in class etomica.veos.bigdecimal.EulerPhi: Compute phi(n).
at(int) - Method in class etomica.veos.bigdecimal.Factorial: Compute the factorial of the non-negative integer.
at(int) - Method in class etomica.veos.bigdecimal.Harmonic: The Harmonic number at the index specified
at(int) - Method in class etomica.veos.bigdecimal.PartitionsP: return the number of partitions of i
at(int) - Method in class etomica.veos.bigdecimal.Prime: return the ithprime
atan(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The inverse trigonometric tangent.
aTarget - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
aTarget - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
aTarget - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
aTarget - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
atom - Variable in class etomica.association.MCMoveDimer
atom - Variable in class etomica.association.MCMoveDimerRotate
atom - Variable in class etomica.association.MCMoveSmer
atom - Variable in class etomica.association.MCMoveSmerRotate
Atom - Class in etomica.atom: Atom that represents a physical atom with a position.
Atom(ISpace, IAtomType) - Constructor for class etomica.atom.Atom
Atom(ISpace) - Constructor for class etomica.atom.Atom: Makes a simple atom for the given space.
atom - Variable in class etomica.atom.AtomSetSinglet
atom - Variable in class etomica.atom.MoleculeSetSinglet
atom - Variable in class etomica.box.BoxAtomEvent
atom - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
atom - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
atom - Variable in class etomica.integrator.IntegratorHard.Agent
atom() - Method in class etomica.integrator.IntegratorHard.Agent
atom - Variable in class etomica.integrator.mcmove.MCMoveAtom
atom - Variable in class etomica.integrator.mcmove.MCMoveDimer
atom - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
atom - Variable in class etomica.models.hexane.MCMoveCBMC
atom - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
atom - Variable in class etomica.potential.PotentialReactive.BondChangeData
atom - Variable in class etomica.spin.MCMoveSpinFlip
atom - Variable in class etomica.virial.MeterVirialExternalFieldSW.Near
atom0 - Variable in class etomica.atom.AtomPair
atom0 - Variable in class etomica.atom.MoleculePair
atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupled
atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
atom0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
atom1 - Variable in class etomica.association.MCMoveDimer
atom1 - Variable in class etomica.association.MCMoveDimerRotate
atom1 - Variable in class etomica.atom.AtomPair
atom1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
atom1 - Variable in class etomica.atom.MoleculePair
atom1 - Variable in class etomica.data.DataSourceAtomDistance
atom1 - Variable in class etomica.integrator.mcmove.MCMoveDimer
atom1 - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupled
atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
atom1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
ATOM1_INDEX - Static variable in class etomica.util.Debug: Atom index of first atom of interest.
atom2 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
atom2 - Variable in class etomica.data.DataSourceAtomDistance
atom2 - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
atom2 - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
ATOM2_INDEX - Static variable in class etomica.util.Debug: Atom index of second atom of interest.
atom_aC_A - Static variable in class etomica.action.IntegratorDimerApproach
atom_aC_B - Static variable in class etomica.action.IntegratorDimerApproach
atom_aH_A - Static variable in class etomica.action.IntegratorDimerApproach
atom_aH_B - Static variable in class etomica.action.IntegratorDimerApproach
atom_H1_A - Static variable in class etomica.action.IntegratorDimerApproach
ATOM_IN_FRAME - Static variable in class org.jmol.viewer.JmolConstants
atom_O_A - Static variable in class etomica.action.IntegratorDimerApproach
atom_O_B - Static variable in class etomica.action.IntegratorDimerApproach
ATOM_SIZE - Static variable in class etomica.util.Debug: The minimum allowable distance between Atoms.
ATOM_SLABBED - Static variable in class org.jmol.viewer.JmolConstants
AtomAction - Interface in etomica.action: Interface for a class that can perform an action on an atom.
AtomActionRandomizeVelocity - Class in etomica.action: Action that sets the velocity vector of a given atom to a randomly chosen value sampled from a Boltzmann distribution.
AtomActionRandomizeVelocity(double, IRandom) - Constructor for class etomica.action.AtomActionRandomizeVelocity: Constructs class to assign velocities according to the given temperature.
atomActionRandomizeVelocity - Variable in class etomica.action.BoxRandomizeMomenta
atomActionRandomizeVelocity - Variable in class etomica.integrator.IntegratorMD
AtomActionRotateBy - Class in etomica.action: Performs RIGHT-HANDED rotations of an atom about the x-, y-, and z-axes by the specified angles (roll, pitch, and yaw angles, respectively) in radians.
AtomActionRotateBy(ISpace) - Constructor for class etomica.action.AtomActionRotateBy
atomActionRotateBy - Variable in class etomica.action.IntegratorDimerApproach
AtomActionTransformed - Class in etomica.models.nitrogen: Moves (translates) an atom by a specified vector amount.
AtomActionTransformed(ISpace) - Constructor for class etomica.models.nitrogen.AtomActionTransformed
AtomActionTransformed - Class in etomica.paracetamol: Moves (translates) an atom by a specified vector amount.
AtomActionTransformed(ISpace) - Constructor for class etomica.paracetamol.AtomActionTransformed
AtomActionTranslateBy - Class in etomica.action: Moves (translates) an atom by a specified vector amount.
AtomActionTranslateBy(ISpace) - Constructor for class etomica.action.AtomActionTranslateBy
atomActionTranslateBy - Variable in class etomica.action.IntegratorDimerApproach
atomActionTranslateTo - Variable in class etomica.config.ConfigurationLattice
atomActionTranslateTo - Variable in class etomica.config.ConfigurationLatticeSimple
atomActionTranslateTo - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
atomActionTranslateTo - Variable in class etomica.normalmode.CoordinateDefinition
atomActionTranslateTo - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
atomActionTranslateTo - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
atomAdded(IAtom) - Method in class etomica.box.BoxEventManager
AtomAgent(ISpace) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.AtomAgent
AtomAgent(ISpace) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion.AtomAgent
atomAgent0 - Variable in class etomica.dimer.IntegratorDimerMin
atomAgent0 - Variable in class etomica.dimer.IntegratorDimerRT
atomAgent1 - Variable in class etomica.dimer.IntegratorDimerRT
atomAgent2 - Variable in class etomica.dimer.IntegratorDimerRT
atomAgentClass - Variable in class etomica.box.BoxAgentSourceAtomManager
atomAgentManager - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
atomAgentManager - Variable in class etomica.graphics.BondListener
atomAgentManager - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
atomAgentManager - Variable in class etomica.potential.EwaldSummation
atomAgentManager - Variable in class etomica.potential.EwaldSumMolecules
atomAgentManager - Variable in class etomica.potential.P1HarmonicSite
atomAgentManager - Variable in class etomica.threaded.PotentialCalculationForceSumThreaded
atomAgentMin - Variable in class etomica.dimer.IntegratorDimerMin
atomAgentSource - Variable in class etomica.box.BoxAgentSourceAtomManager
atomArray - Variable in class etomica.atom.iterator.TripletInnerSequential
AtomArrayList - Class in etomica.atom
AtomArrayList() - Constructor for class etomica.atom.AtomArrayList
AtomArrayList(int) - Constructor for class etomica.atom.AtomArrayList
atomColor - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
atomCount - Variable in class etomica.modules.entropylottery.MeterEntropy
AtomDecompositionMD - Class in etomica.threads
AtomDecompositionMD() - Constructor for class etomica.threads.AtomDecompositionMD
AtomFilter - Interface in etomica.atom: Interface for a class that screens atoms according to some criterion.
atomFilter - Variable in class etomica.graphics.DisplayBox
AtomFilterChainLength - Class in etomica.modules.chainequilibrium
AtomFilterChainLength(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.AtomFilterChainLength
AtomFilterChainLength.LengthAgent - Class in etomica.modules.chainequilibrium
AtomFilterCollective - Interface in etomica.atom: Filter that needs to be informed whenever something has changed and the filtered status of atoms should be redetermined.
AtomFilterInCylinder(IBoundary, P1HardMovingBoundary, double) - Constructor for class etomica.modules.pistoncylinder.ApiFilteredCylinder.AtomFilterInCylinder
AtomFilterInShape - Class in etomica.atom: Filter that accepts atom if it is inside a specified Shape instance.
AtomFilterInShape(Shape) - Constructor for class etomica.atom.AtomFilterInShape: Create filter in which position definition is given by atom's type.
AtomFilterLiquid - Class in etomica.modules.droplet
AtomFilterLiquid(ISpace, IDataSource) - Constructor for class etomica.modules.droplet.AtomFilterLiquid
AtomFilterLiquidAtomic - Class in etomica.modules.droplet
AtomFilterLiquidAtomic(PotentialMasterList, IBox) - Constructor for class etomica.modules.droplet.AtomFilterLiquidAtomic
AtomFilterStatic - Class in etomica.atom
atomGroupAction - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
atomGroupAction - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
atomGroupAction - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
atomGroupAction - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
atomGroupAction - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
atomGroupAction - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
atomGroupAction - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
atomGroupAction - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
atomGroupAction - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
atomGroupAction - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
atomGroupActionRotateBy - Variable in class etomica.action.IntegratorDimerApproach
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
atomGroupActionTranslate - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
atomGroupActionTranslateBy - Variable in class etomica.action.IntegratorDimerApproach
AtomGroupVelocityAverage - Class in etomica.atom: Calculates the mass average velocity over a set of atoms.
AtomGroupVelocityAverage(ISpace) - Constructor for class etomica.atom.AtomGroupVelocityAverage
AtomHydrogen - Class in etomica.atom
AtomHydrogen(ISpace, IAtomTypeOriented, double) - Constructor for class etomica.atom.AtomHydrogen
atomicMass - Static variable in class org.jmol.util.Elements
atomicNumber - Variable in class etomica.chem.elements.ElementChemical
atomicPotentials - Variable in class etomica.potential.PotentialMasterLrc
atomicTensor(IAtom, IAtom) - Method in interface etomica.models.water.P2Water4PSoft.AtomicTensorAtomicPair
atomicTensor(IAtom, IAtom) - Method in interface etomica.normalmode.LatticeSumMolecularCrystal.AtomicTensorAtomicPair
atomicTensorAtomicPair - Variable in class etomica.normalmode.NormalModesMolecular
atomicToMolecularD(IMolecule, IMolecule) - Method in class etomica.models.water.P2Water4PSoft
atomicToMolecularD(LatticeSumMolecularCrystal.AtomicTensorAtomicPair, IMolecule, IMolecule) - Method in class etomica.normalmode.LatticeSumMolecularCrystal
atomid - Static variable in class org.jmol.script.Token
ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C2 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C4 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C5 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C5M - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C6 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C7 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_C8 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_MAX - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N1 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N2 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N3 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N4 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N6 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N7 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_N9 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O1 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O1P - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O2 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O2P - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O4 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_O6 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_OP1 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_OP2 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_S4 - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_SG - Static variable in class org.jmol.viewer.JmolConstants
ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JmolConstants
atomindex - Static variable in class org.jmol.script.Token
AtomIterator - Interface in etomica.atom.iterator: Interface for classes that loop over a set of atoms.
atomIterator - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
atomIterator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
atomIterator - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
atomIterator - Variable in class etomica.threaded.atom.PotentialMasterListWorker
atomIterator - Variable in class etomica.threaded.domain.PotentialMasterListWorker
AtomIterator0() - Constructor for class etomica.potential.PotentialMaster.AtomIterator0
AtomIteratorAllLeafType - Class in etomica.atom.iterator: Iterator for all the molecules of a set of species in a box.
AtomIteratorAllLeafType(IAtomType[]) - Constructor for class etomica.atom.iterator.AtomIteratorAllLeafType
AtomIteratorArrayList - Class in etomica.atom.iterator: An atom iterator of the elements from an AtomArrayList (in proper sequence).
AtomIteratorArrayList(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList: Constructs new iterator with an empty list.
AtomIteratorArrayList(IteratorDirective.Direction, int) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList: Constructs new iterator set to iterate given list (upon reset).
AtomIteratorArrayList(IteratorDirective.Direction, int, AtomToIndex, AtomToAtomLeafList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
AtomIteratorArrayListAdjacent - Class in etomica.atom.iterator: Returns one or both of the atoms adjacent to a specified atom in its parent's child list.
AtomIteratorArrayListAdjacent(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Constructor gives iterator not ready for iteration.
AtomIteratorArrayListAdjacent(IteratorDirective.Direction, AtomToIndex, AtomToAtomLeafList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListAdjacent
AtomIteratorArrayListSimple - Class in etomica.atom.iterator: An atom iterator of the elements from an AtomArrayList (in proper sequence).
AtomIteratorArrayListSimple() - Constructor for class etomica.atom.iterator.AtomIteratorArrayListSimple: Constructs new iterator with an empty list.
AtomIteratorArrayListSimple(IAtomList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListSimple: Constructs new iterator set to iterate given list (upon reset).
AtomIteratorAtomDependent - Interface in etomica.atom.iterator: Interface for an atom iterator that can be altered by setting of an atom.
AtomIteratorBasis - Class in etomica.atom.iterator: Elementary basis-dependent iterator that gives atoms meeting specification of a basis and a target.
AtomIteratorBasis() - Constructor for class etomica.atom.iterator.AtomIteratorBasis: Constructor makes iterator in an unset condition; must set basis and call reset before beginning iteration.
AtomIteratorBasisAdjustableStart - Class in etomica.atom.iterator: Elementary basis-dependent iterator that gives atoms meeting specification of a basis and a target.
AtomIteratorBasisAdjustableStart() - Constructor for class etomica.atom.iterator.AtomIteratorBasisAdjustableStart: Constructor makes iterator in an unset condition; must set basis and call reset before beginning iteration.
AtomIteratorBasisDependent - Interface in etomica.atom.iterator
AtomIteratorBasisFilteredType - Class in etomica.atom.iterator
AtomIteratorBasisFilteredType(IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType
AtomIteratorBasisFilteredType2 - Class in etomica.atom.iterator: This iterator returns atoms that are one of two types.
AtomIteratorBasisFilteredType2(IAtomType, IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType2
AtomIteratorBoxDependent - Interface in etomica.atom.iterator: Interface indicating that an atom iterator can determine appropriate atoms for iteration given an arbitrary box.
AtomIteratorBruteForce(IBox) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
AtomIteratorCell - Class in etomica.nbr.cell: Returns occupants of all cells as iterates.
AtomIteratorCell(int, BoxAgentManager) - Constructor for class etomica.nbr.cell.AtomIteratorCell: Constructor makes iterator that must have box specified and then be reset() before iteration.
AtomIteratorLeafAtoms - Class in etomica.atom.iterator: Iterator that will loop over all leaf atoms in a box.
AtomIteratorLeafAtoms() - Constructor for class etomica.atom.iterator.AtomIteratorLeafAtoms: Creates iterator with no box specified.
AtomIteratorLeafAtoms(IBox) - Constructor for class etomica.atom.iterator.AtomIteratorLeafAtoms: Creates iterator conditioned to give all leaf atoms of the specified box.
AtomIteratorLeafFilteredType - Class in etomica.atom.iterator
AtomIteratorLeafFilteredType(IBox, IAtomType) - Constructor for class etomica.atom.iterator.AtomIteratorLeafFilteredType
AtomIteratorNbr(NeighborListManager) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
AtomIteratorNbrCell(double, BoxAgentManager<? extends BoxCellManager>, IBox) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
AtomIteratorNull - Class in etomica.atom.iterator: Static iterator that returns no atoms.
AtomIteratorSinglet - Class in etomica.atom.iterator: Iterator that expires after returning a single atom, which is specified by a call to the setAtom method, or via the constructor.
AtomIteratorSinglet() - Constructor for class etomica.atom.iterator.AtomIteratorSinglet: Constructs iterator without defining atom.
AtomIteratorSinglet(IAtom) - Constructor for class etomica.atom.iterator.AtomIteratorSinglet: Constructs iterator specifying that it return the given atom.
atomLeafAgentManager - Variable in class etomica.association.MCMoveVolumeAssociated
AtomLeafAgentManager<E> - Class in etomica.atom: AtomAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every leaf Atom in a box.
AtomLeafAgentManager(AtomLeafAgentManager.AgentSource<E>, IBox, Class) - Constructor for class etomica.atom.AtomLeafAgentManager
AtomLeafAgentManager.AgentIterator<E> - Class in etomica.atom: Iterator that loops over the agents, skipping null elements
AtomLeafAgentManager.AgentSource<E> - Interface in etomica.atom: Interface for an object that wants an agent associated with each Atom in a Box.
AtomLeafDynamic - Class in etomica.atom
AtomLeafDynamic(ISpace, IAtomType) - Constructor for class etomica.atom.AtomLeafDynamic
atomLeafIndexChanged(IAtom, int) - Method in class etomica.box.BoxEventManager
AtomLeafsetIterator - Interface in etomica.atom.iterator: Interface for classes that loop over a set of atoms.
atomList - Variable in class etomica.atom.AtomArrayList
atomList - Variable in class etomica.atom.iterator.ANIntragroupExchange
atomList - Variable in class etomica.models.hexane.MCMoveCBMC
atomLists - Variable in class etomica.atom.iterator.ANIntergroupCoupled
AtomListWrapper - Class in etomica.atom: AtomSet formed by wrapping an AtomArrayList.
AtomListWrapper() - Constructor for class etomica.atom.AtomListWrapper: Wraps a new atom array of the given length.
AtomListWrapper(IAtomList) - Constructor for class etomica.atom.AtomListWrapper: Makes a new instance holding the atoms in the given atom set.
AtomListWrapper(AtomArrayList) - Constructor for class etomica.atom.AtomListWrapper: Wraps the given atom array.
atomMove - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
atomMove - Variable in class etomica.normalmode.SimEinStep1
atomMove - Variable in class etomica.normalmode.SimEinStep1HCP
atomMove - Variable in class etomica.normalmode.SimEinStep2
atomMove - Variable in class etomica.normalmode.SimEinStep2HCP
atomMove - Variable in class etomica.normalmode.SimLJHTTISuper
atomMove - Variable in class etomica.normalmode.SimLJHTTISuperHCP
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphere
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
atomMove - Variable in class etomica.normalmode.SimOverlapSSnxy
atomMoveRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
atomMoveTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
atomname - Static variable in class org.jmol.script.Token
AtomNeighborLists - Class in etomica.nbr.list: Class used to maintain neighbor lists.
AtomNeighborLists() - Constructor for class etomica.nbr.list.AtomNeighborLists: Constructs sequencer for the given atom.
atomno - Static variable in class org.jmol.script.Token
atomNumber - Variable in class etomica.modules.materialfracture.StrainColorScheme
atomNumberMod - Variable in class etomica.modules.materialfracture.StrainColorScheme
AtomOriented - Class in etomica.atom
AtomOriented(ISpace, IAtomType) - Constructor for class etomica.atom.AtomOriented
AtomOriented(ISpace, IAtomType, boolean) - Constructor for class etomica.atom.AtomOriented
AtomOrientedDynamic - Class in etomica.atom
AtomOrientedDynamic(ISpace, IAtomType) - Constructor for class etomica.atom.AtomOrientedDynamic
AtomOrientedDynamic(ISpace, IAtomType, boolean) - Constructor for class etomica.atom.AtomOrientedDynamic
AtomOrientedQuaternion - Class in etomica.atom
AtomOrientedQuaternion(ISpace, IAtomType) - Constructor for class etomica.atom.AtomOrientedQuaternion
AtomPair - Class in etomica.atom: Data structure that contains two mutable atom instances.
AtomPair() - Constructor for class etomica.atom.AtomPair
AtomPair(IAtom, IAtom) - Constructor for class etomica.atom.AtomPair
atomPair - Variable in class etomica.nbr.list.PotentialMasterList
atomPair - Variable in class etomica.potential.PotentialMasterMonatomic
atomPair - Variable in class etomica.threaded.atom.PotentialMasterListWorker
atomPair - Variable in class etomica.threaded.domain.PotentialMasterListWorker
AtomPairSet - Class in etomica.virial: Class that holds a set of atom pairs.
AtomPairSet(IMoleculeList) - Constructor for class etomica.virial.AtomPairSet: Constructor for AtomPairSet.
atompicking - Static variable in class org.jmol.script.Token
atomPosDef - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
AtomPositionCOM - Class in etomica.atom: Calculates the center of mass (COM) over a set of atoms.
AtomPositionCOM(ISpace) - Constructor for class etomica.atom.AtomPositionCOM
atomPositionCOM - Variable in class etomica.integrator.IntegratorRigidIterative
atomPositionCOM - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
atomPositionCOM - Variable in class etomica.models.water.OrientationCalcWater3P
atomPositionCOM - Variable in class etomica.models.water.OrientationCalcWater4P
atomPositionCOM - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
AtomPositionFirstAtom - Class in etomica.atom: Returns the position of the first child leaf atom.
AtomPositionFirstAtom() - Constructor for class etomica.atom.AtomPositionFirstAtom
AtomPositionGeometricCenter - Class in etomica.atom: Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenter(ISpace) - Constructor for class etomica.atom.AtomPositionGeometricCenter
AtomPositionGeometricCenterAlkaneEH - Class in etomica.atom: Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenterAlkaneEH(ISpace, ISpecies) - Constructor for class etomica.atom.AtomPositionGeometricCenterAlkaneEH
AtomPositionGeometricCenterPBC - Class in etomica.atom: Calculates the geometric center over a set of atoms.
AtomPositionGeometricCenterPBC(ISpace, IBoundary) - Constructor for class etomica.atom.AtomPositionGeometricCenterPBC
AtomPotential1ListSource(PotentialMasterList) - Constructor for class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
AtomPotentialList - Class in etomica.nbr.list: Class used to maintain list of whether each 1-body potential that applies to an AtomType is currently in effect or not for an Atom.
AtomPotentialList() - Constructor for class etomica.nbr.list.AtomPotentialList: Constructs sequencer for the given atom.
atomproperty - Static variable in class org.jmol.script.Token
atomRemoved(IAtom) - Method in class etomica.box.BoxEventManager
atoms - Variable in class etomica.atom.iterator.ANIntergroupCoupled
atoms - Variable in class etomica.atom.iterator.ANIntergroupExchange
atoms - Variable in class etomica.atom.iterator.ANIntragroupExchange
atoms - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
atoms - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
atoms - Variable in class etomica.potential.PotentialMolecularMonatomic
atoms - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
atoms - Variable in class etomica.virial.CoordinatePairMoleculeSet
atoms - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
atoms - Variable in class etomica.virial.MCMoveClusterRingScale
atoms - Static variable in class org.jmol.script.Token
Atomset3IteratorIndexList - Class in etomica.atom.iterator: Atomset Iterator that iterates over set-of-three atoms
Atomset3IteratorIndexList(int[][]) - Constructor for class etomica.atom.iterator.Atomset3IteratorIndexList: Constructs iterator without defining set of atoms.
Atomset4IteratorIndexList - Class in etomica.atom.iterator: Atomset Iterator that iterates over set-of-four atoms
Atomset4IteratorIndexList(int[][]) - Constructor for class etomica.atom.iterator.Atomset4IteratorIndexList: Constructs iterator without defining set of atoms.
atomSetA - Variable in class etomica.action.IntegratorDimerApproach
AtomSetAllMolecules - Class in etomica.box
AtomSetAllMolecules() - Constructor for class etomica.box.AtomSetAllMolecules
AtomsetArray - Class in etomica.atom: AtomSet formed by wrapping an Atom array.
AtomsetArray(int) - Constructor for class etomica.atom.AtomsetArray: Wraps a new atom array of the given length.
AtomsetArray(IAtomList) - Constructor for class etomica.atom.AtomsetArray: Makes a new instance holding the atoms in the given atom set.
AtomsetArray(AtomsetArray) - Constructor for class etomica.atom.AtomsetArray: Copy constructor, wrapping a new array unique to this instance but holding the same atoms as the given atom set.
AtomsetArray(IAtom[]) - Constructor for class etomica.atom.AtomsetArray: Wraps the given atom array.
atomsetArrayList - Variable in class etomica.threaded.atom.PotentialMasterListWorker
atomsetArrayList - Variable in class etomica.threaded.domain.PotentialMasterListWorker
atomSetB - Variable in class etomica.action.IntegratorDimerApproach
AtomsetIterator - Interface in etomica.atom.iterator: Interface for classes that loop over a set of atoms.
AtomsetIteratorAllLeafAtoms - Class in etomica.atom.iterator: Iterator for all the molecules of a set of species in a box.
AtomsetIteratorAllLeafAtoms() - Constructor for class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
AtomsetIteratorBasisDependent - Interface in etomica.atom.iterator: Interface for an AtomIterator that can be conditioned with target and basis atoms.
AtomsetIteratorBoxDependent - Interface in etomica.atom.iterator: Interface indicating that an iterator can determine appropriate atoms for iteration given an arbitrary box.
AtomsetIteratorCellular - Interface in etomica.nbr.cell: Interface for atomset iterators that use cell-based neighbor lists for iteration.
AtomsetIteratorDirectable - Interface in etomica.atom.iterator: Interface for an iterator that can interpret specification of direction UP or DOWN.
AtomsetIteratorPDT - Interface in etomica.atom.iterator: This is an interface for iterators that are box dependent, directable, and targetable.
AtomsetIteratorTargetable - Interface in etomica.atom.iterator: Interface for an iterator that can be targeted at one or more atoms.
AtomSetSinglet - Class in etomica.atom: Data structure that contains a single mutable atom instance.
AtomSetSinglet() - Constructor for class etomica.atom.AtomSetSinglet
AtomSetSinglet(IAtom) - Constructor for class etomica.atom.AtomSetSinglet
atomSetSinglet - Variable in class etomica.atom.iterator.ApiIntergroup
atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple
atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorSinglet
atomSetSinglet - Variable in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
atomSetSinglet - Variable in class etomica.atom.iterator.MoleculeIteratorSinglet
atomSetSinglet - Variable in class etomica.graphics.BondListener
atomSetSinglet - Variable in class etomica.integrator.IntegratorHard.Agent
atomSetSinglet - Variable in class etomica.modules.pistoncylinder.IntegratorHardPiston
atomSetSinglet - Variable in class etomica.nbr.cell.AtomIteratorCell
atomSetSinglet - Variable in class etomica.nbr.list.NeighborListManager
atomSetSinglet - Variable in class etomica.nbr.list.PotentialMasterList
atomSetSinglet - Variable in class etomica.nbr.PotentialGroupNbr
atomSetSinglet - Variable in class etomica.nbr.site.PotentialMasterSite
atomSetSinglet - Variable in class etomica.potential.PotentialMasterMonatomic
atomSetSinglet - Variable in class etomica.threaded.atom.PotentialMasterListWorker
atomSetSinglet - Variable in class etomica.threaded.domain.PotentialMasterListWorker
atomSinglet - Variable in class etomica.freeenergy.npath.MCMoveAtomNPath
atomSinglet - Variable in class etomica.normalmode.MCMoveAtomCoupled
AtomSite - Class in etomica.nbr.site: Site used to form array of cells for cell-based neighbor listing.
AtomSite(int) - Constructor for class etomica.nbr.site.AtomSite
atomSource - Variable in class etomica.association.MCMoveDimer
atomSource - Variable in class etomica.association.MCMoveDimerRotate
atomSource - Variable in class etomica.association.MCMoveSmer
atomSource - Variable in class etomica.association.MCMoveSmerRotate
AtomSource - Interface in etomica.atom: Interface for objects when return atoms (meeting some specification) from a box.
atomSource - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
atomSource - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
atomSource - Variable in class etomica.integrator.mcmove.MCMoveAtom
atomSource - Variable in class etomica.integrator.mcmove.MCMoveDimer
atomSource - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
atomSource - Variable in class etomica.models.hexane.MCMoveReptate
atomSource - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupled
atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
AtomSourceRandomDimer - Class in etomica.association
AtomSourceRandomDimer() - Constructor for class etomica.association.AtomSourceRandomDimer
AtomSourceRandomLeaf - Class in etomica.atom: AtomSource that returns a completely random leaf atom.
AtomSourceRandomLeaf() - Constructor for class etomica.atom.AtomSourceRandomLeaf
AtomSourceRandomMonomer - Class in etomica.association
AtomSourceRandomMonomer() - Constructor for class etomica.association.AtomSourceRandomMonomer
AtomSourceRandomSmer - Class in etomica.association
AtomSourceRandomSmer() - Constructor for class etomica.association.AtomSourceRandomSmer
AtomSourceRandomSpecies - Class in etomica.atom: AtomSource that returns a completely random leaf atom.
AtomSourceRandomSpecies() - Constructor for class etomica.atom.AtomSourceRandomSpecies
AtomSourceRandomSpecies(IRandom, ISpecies) - Constructor for class etomica.atom.AtomSourceRandomSpecies
atomSpeciesA - Variable in class etomica.normalmode.MCMoveAtomSuperBox
atomSpeciesB - Variable in class etomica.normalmode.MCMoveAtomSuperBox
atomsPerGroup - Variable in class etomica.species.SpeciesSpheres
AtomTag() - Constructor for class etomica.modules.chainequilibrium.MeterChainLength.AtomTag
AtomTimeAction() - Constructor for class etomica.integrator.IntegratorAnalytic.AtomTimeAction
AtomToAtomLeafList - Interface in etomica.atom: Interface for class that determines an AtomArrayList given an atom.
atomToAtomSet - Variable in class etomica.atom.iterator.MpiIntraspecies1A
AtomToAtomSetFixed - Class in etomica.atom
AtomToAtomSetFixed() - Constructor for class etomica.atom.AtomToAtomSetFixed
AtomToIndex - Interface in etomica.atom: Interface for class that associates an integer with an atom.
AtomToIndexChild - Class in etomica.atom: Defines the index as the Atom's node's index.
AtomToIndexChild() - Constructor for class etomica.atom.AtomToIndexChild
AtomToParentChildList - Class in etomica.atom
AtomToParentChildList() - Constructor for class etomica.atom.AtomToParentChildList
atomToPosVec(IAtom) - Static method in class etomica.potential.P2WaterPotentialsJankowski
atomTranslator - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
atomTranslator - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
atomType - Variable in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
atomtype - Static variable in class org.jmol.script.Token
atomTypeAddedNotify(IAtomType) - Method in class etomica.simulation.Simulation
AtomTypeAgentManager - Class in etomica.atom: AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every AtomType in a box.
AtomTypeAgentManager(AtomTypeAgentManager.AgentSource) - Constructor for class etomica.atom.AtomTypeAgentManager
AtomTypeAgentManager(AtomTypeAgentManager.AgentSource, ISimulation) - Constructor for class etomica.atom.AtomTypeAgentManager
AtomTypeAgentManager.AgentIterator - Class in etomica.atom: Iterator that loops over the agents, skipping null elements
AtomTypeAgentManager.AgentSource - Interface in etomica.atom: Interface for an object that wants an agent associated with each AtomType in a Simulation.
atomTypeIndexChanged(IAtomType, int) - Method in class etomica.simulation.SimulationEventManager
AtomTypeLeaf - Class in etomica.atom: Type for an atom that is a leaf in the species hierarchy.
AtomTypeLeaf(IElement) - Constructor for class etomica.atom.AtomTypeLeaf
atomTypeMaxIndexChanged(int) - Method in class etomica.simulation.SimulationEventManager
atomTypeOrientedManager - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
AtomTypeOrientedSphere - Class in etomica.atom: Atom type for a sphere that has some feature depending upon an orientation coordinate.
AtomTypeOrientedSphere(IElement, ISpace) - Constructor for class etomica.atom.AtomTypeOrientedSphere
atomTypeRemovedNotify(IAtomType) - Method in class etomica.simulation.Simulation
atomTypes - Variable in class etomica.potential.P2SquareWellRobust
atomTypes - Variable in class etomica.species.SpeciesSpheresCustom
atomtypes - Static variable in class org.jmol.script.Token
AtomTypeSpheroPolyhedron - Class in etomica.atom
AtomTypeSpheroPolyhedron(IElement, ISpace, List<IVector>, double) - Constructor for class etomica.atom.AtomTypeSpheroPolyhedron
atomx - Static variable in class org.jmol.script.Token
atomy - Static variable in class org.jmol.script.Token
atomz - Static variable in class org.jmol.script.Token
atry - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
atry - Variable in class etomica.util.numerical.NonLinearCurveFitting
ATTO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-18.
auto - Static variable in class org.jmol.script.Token
autobond - Static variable in class org.jmol.script.Token
autofps - Static variable in class org.jmol.script.Token
autoRowLabels - Variable in class etomica.graphics.DisplayTable
aveCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
AVERAGE - Static variable in class etomica.data.AccumulatorAverage
average - Variable in class etomica.data.AccumulatorAverage
AVERAGE - Static variable in class etomica.data.AccumulatorAverageBlockless
average - Variable in class etomica.data.AccumulatorAverageBlockless
AVERAGE - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
average - Static variable in class org.jmol.script.Token
averageBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
averages - Variable in class etomica.data.AccumulatorAverageCollapsingLog
AVG - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
AVG - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
avgEnergy - Variable in class etomica.simulation.prototypes.LjMd3D
avgEnergy - Variable in class etomica.thermointegration.LjMc3D
avgStat - Variable in class etomica.virial.overlap.DataVirialOverlap
AVOGADRO - Static variable in class etomica.util.Constants: Avogadro's number, 6.02214129(27)e23 molecules/mole.
axes - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
axes - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
AXES - Static variable in class g3dsys.control.G3DSys
Axes - Class in g3dsys.images
Axes(G3DSys, short) - Constructor for class g3dsys.images.Axes
axes - Static variable in class org.jmol.script.Token
AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
axescolor - Static variable in class org.jmol.script.Token
axesmode - Static variable in class org.jmol.script.Token
axesmolecular - Static variable in class org.jmol.script.Token
axesorientationrasmol - Static variable in class org.jmol.script.Token
axesscale - Static variable in class org.jmol.script.Token
axesTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
axesunitcell - Static variable in class org.jmol.script.Token
axeswindow - Static variable in class org.jmol.script.Token
axis - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
axis - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
axis - Variable in class etomica.models.nitrogen.TestRotationVector
axis - Variable in class etomica.modules.droplet.AtomFilterLiquid
axis - Variable in class etomica.modules.droplet.ConfigurationDroplet
axis - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
axis - Variable in class etomica.virial.ClusterCoupledAtomFlipped
axis - Variable in class etomica.virial.MCMoveClusterRotateCH3
axis - Static variable in class org.jmol.script.Token
axis0 - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
axis0 - Variable in class etomica.virial.MCMoveClusterAtomHSRing
axis0Prime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
axis1color - Static variable in class org.jmol.script.Token
axis2color - Static variable in class org.jmol.script.Token
axis3color - Static variable in class org.jmol.script.Token
AxisAngle4f - Class in org.jmol.util: A 4 element axis angle represented by single precision floating point x,y,z,angle components.
AxisAngle4f() - Constructor for class org.jmol.util.AxisAngle4f: Constructs and initializes a AxisAngle4f to (0,0,1,0).
axisNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
axisNormPrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
axisNX - Static variable in class org.jmol.viewer.JmolConstants
axisNY - Static variable in class org.jmol.viewer.JmolConstants
axisNZ - Static variable in class org.jmol.viewer.JmolConstants
axisX - Static variable in class org.jmol.viewer.JmolConstants
axisY - Static variable in class org.jmol.viewer.JmolConstants
axisZ - Static variable in class org.jmol.viewer.JmolConstants

B

B - Variable in class etomica.conjugategradient.ConjugateGradients
B - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
B - Variable in class etomica.conjugategradient.SteepestDescent
b - Variable in class etomica.dimer.P1LepsHarmonic
B - Variable in class etomica.meam.PotentialCuLREP
B - Variable in class etomica.meam.PotentialEFS
b - Variable in class etomica.models.co2.P2CO2Hellmann
b - Variable in class etomica.modules.rheology.IntegratorPolymer
b - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
B - Variable in class etomica.potential.P2HePCKLJS
b - Static variable in class etomica.potential.P2HePCKLJS
b - Variable in class etomica.potential.P2NitrogenHellmann
b - Variable in class etomica.potential.P2WaterPotentialsJankowski
B - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
b - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
b - Variable in class etomica.potential.P3HydrogenManzhos
b - Variable in class etomica.util.numerical.PadeApproximation
b0 - Variable in class etomica.meam.ParameterSetMEAM
b1 - Variable in class etomica.meam.ParameterSetMEAM
B1 - Variable in class etomica.models.nitrogen.P2Nitrogen
B1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
B1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
B10HS(double) - Static method in class etomica.virial.cluster.Standard
B11HS(double) - Static method in class etomica.virial.cluster.Standard
B12HS(double) - Static method in class etomica.virial.cluster.Standard
b2 - Variable in class etomica.meam.ParameterSetMEAM
B2 - Variable in class etomica.modules.adsorption.VEOS3SW
B2(double, double) - Static method in class etomica.modules.vle.LJQB2: Returns B2 for the LJ+quadrupole model.
B2(double) - Static method in class etomica.statmech.LennardJones: Returns the 2nd virial coefficient.
B2 - Static variable in class etomica.virial.cluster.Standard
B2 - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
B2Fit - Class in etomica.modules.vle
B2Fit() - Constructor for class etomica.modules.vle.B2Fit
B2Fit.Applet - Class in etomica.modules.vle
B2Fit.FunctionB2LJQ - Class in etomica.modules.vle: Function using LJQB2 to evaluate B2 as a function of Q, epsilon, sigma and T.
B2Fit.FunctionMayerB2LJQ - Class in etomica.modules.vle: Function using Mayer sampling to evaluate B2 as a function of Q, epsilon, sigma and T.
B2ForSphericallySymmetricUByTrapezoidRule - Class in etomica.virial
B2ForSphericallySymmetricUByTrapezoidRule() - Constructor for class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
B2Hash - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
B2HS(double) - Static method in class etomica.virial.cluster.Standard
B2Ionic - Class in etomica.virial: two points cluster diagrams calculation Integral I2,S2,mean activity coefficient,osmotic coefficient of ionic solution via single integrals include cycle diagram(=>DHLL); (k0); (k2);(kn+n) =0, k-bond, =1, modified q-bond,etc, m>3,two diagrams are added up to evaluate s = parameter * c^2 * I ds/dc = parameter * ( 2*c*I + c^2 * dI/dc) all are in simulation units contains "linear step in sqrt(c)" && "linear step in c"
B2Ionic() - Constructor for class etomica.virial.B2Ionic
B2SW(double, double, double) - Static method in class etomica.virial.cluster.Standard
b3 - Variable in class etomica.meam.ParameterSetMEAM
B3 - Variable in class etomica.modules.adsorption.VEOS3SW
B3ForSphericallySymmetricU - Class in etomica.virial: Compute B3 for a spherically symmetric potential to within a given tolerance, specified with getConvergece(), by either FFT or FFT and one layer of quadrature.
B3ForSphericallySymmetricU() - Constructor for class etomica.virial.B3ForSphericallySymmetricU
B3ForSphericallySymmetricU.DampingParams - Class in etomica.virial
B3HS(double) - Static method in class etomica.virial.cluster.Standard
B3LJ - Class in etomica.virial: This is a main method to compute B3 and dB3/dT for Lennard-Jones via FFT It creates a discretization of the Lennard-Jones Mayer function, and computes B3 via FFT.
B3LJ() - Constructor for class etomica.virial.B3LJ
B3NonAddForSphericallySymmetricU - Class in etomica.virial: Computes the classical, non-additive component of B3 for a spherically symmetric potential using quadrature.
B3NonAddForSphericallySymmetricU() - Constructor for class etomica.virial.B3NonAddForSphericallySymmetricU
B3SW(double, double, double) - Static method in class etomica.virial.cluster.Standard
b45 - Variable in class etomica.modules.sam.P1Sinusoidal
B4FFTLJ - Class in etomica.virial: Computes four approximations of B4 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
B4FFTLJ() - Constructor for class etomica.virial.B4FFTLJ
B4HS(double) - Static method in class etomica.virial.cluster.Standard
B5FFTLJ - Class in etomica.virial: Computes four approximations of B5 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
B5FFTLJ() - Constructor for class etomica.virial.B5FFTLJ
B5HS(double) - Static method in class etomica.virial.cluster.Standard
B6FFTLJ - Class in etomica.virial: Modification of FFT Program of B4
B6FFTLJ() - Constructor for class etomica.virial.B6FFTLJ
B6HS(double) - Static method in class etomica.virial.cluster.Standard
B7HS(double) - Static method in class etomica.virial.cluster.Standard
B8HS(double) - Static method in class etomica.virial.cluster.Standard
B9HS(double) - Static method in class etomica.virial.cluster.Standard
B9Optimizer - Class in etomica.util.numerical: Class to determine B9 value that best fit the simulation results
B9Optimizer(String, String) - Constructor for class etomica.util.numerical.B9Optimizer
B9Optimizer.VirialParam - Class in etomica.util.numerical
bA - Static variable in class etomica.models.co2.P2CO2Hellmann
bA - Static variable in class etomica.potential.P2NitrogenHellmann
BACK - Static variable in class etomica.util.Constants.Direction
backbone - Static variable in class org.jmol.script.Token
backgroundColor - Variable in class etomica.graph.view.rasterizer.SVGConverter: Background color for the output images.
backgroundcolor - Static variable in class org.jmol.script.Token
backgroundImage - Variable in class org.jmol.util.GData
backgroundmodel - Static variable in class org.jmol.script.Token
backlit - Static variable in class org.jmol.script.Token
backTrack() - Method in class etomica.graph.isomorphism.AbstractSearchState
backTrack() - Method in interface etomica.graph.isomorphism.SearchState
backTrack() - Method in class etomica.graph.isomorphism.VF2SearchState
backTrack() - Method in class etomica.graph.isomorphism.VFSearchState
backwardDataMap - Variable in class etomica.data.DataSet
bALattice - Variable in class etomica.normalmode.DataSourceMuRoot1
bALattice - Variable in class etomica.normalmode.DataSourceMuRootPMatch
bALattice - Variable in class etomica.normalmode.DataSourcePMu
BALL - Static variable in class g3dsys.control.G3DSys: implemented shapes
Ball - Class in g3dsys.images: Class for drawing spheres (atoms)
Ball(G3DSys, short, float, float, float, float) - Constructor for class g3dsys.images.Ball
Ball(G3DSys, short, Point3f, float) - Constructor for class g3dsys.images.Ball
Bar - Class in etomica.units: The bar unit of pressure, equal to 10^5 N/m^2.
Barye - Class in etomica.units: The barye unit of pressure, equal to 1 dyn/cm^2.
basepair - Static variable in class org.jmol.script.Token
baseUnits() - Method in class etomica.units.systems.UnitSystem
basis - Variable in class etomica.lattice.BravaisLatticeCrystal
Basis - Class in etomica.lattice.crystal: General basis class that hold scaled coordinates of atoms within a unit cell.
Basis(IVector[]) - Constructor for class etomica.lattice.crystal.Basis
basis - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
basis - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
basis - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
basis - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
basis - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
basis - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
basis - Variable in class etomica.models.oneDHardRods.SimDifferentImage
basis - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
basis - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
basis - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
basis - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
basis - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
basis - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
basis - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
basis - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
basis - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
basis - Variable in class etomica.models.oneDHardRods.SimWidomMode
basis - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
basis - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
basis - Variable in class etomica.normalmode.CoordinateDefinition
basis - Variable in class etomica.normalmode.HessianDB
basis - Variable in class etomica.normalmode.LJVacancyMin
basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
basis - Variable in class etomica.normalmode.NormalModes2D
basis - Variable in class etomica.normalmode.NormalModes3D
basis - Variable in class etomica.normalmode.SimBennet
basis - Variable in class etomica.normalmode.SimCalcSLJ
basis - Variable in class etomica.normalmode.SimCalcSMorse
basis - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
basis - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
basis - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
basis - Variable in class etomica.normalmode.SimEinStep1
basis - Variable in class etomica.normalmode.SimEinStep1HCP
basis - Variable in class etomica.normalmode.SimEinStep2
basis - Variable in class etomica.normalmode.SimEinStep2HCP
basis - Variable in class etomica.normalmode.SimHarmonicUmbrella
basis - Variable in class etomica.normalmode.SimLJHTTISuper
basis - Variable in class etomica.normalmode.SimLJHTTISuperHCP
basis - Variable in class etomica.normalmode.SimOverlap
basis - Variable in class etomica.normalmode.SimOverlapLJ
basis - Variable in class etomica.normalmode.SimOverlapLJModule
basis - Variable in class etomica.normalmode.SimOverlapSoftSphere
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
basis - Variable in class etomica.normalmode.SimOverlapSSnxy
basis - Variable in class etomica.normalmode.SimTargetUmbrella
basis - Variable in class etomica.normalmode.SimUmbrella
basis - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
basis - Variable in class etomica.potential.EwaldSummation
basis - Variable in class etomica.potential.P2QChemInterpolated
basis - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
basis - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
basis - Variable in class etomica.potential.P3QChem.DampingParams
BasisBetaSnA5 - Class in etomica.lattice.crystal: Basis that helps construct a beta-tin crystal.
BasisBetaSnA5() - Constructor for class etomica.lattice.crystal.BasisBetaSnA5
BasisBigCell - Class in etomica.normalmode
BasisBigCell(ISpace, Basis, int[]) - Constructor for class etomica.normalmode.BasisBigCell
basisCell - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
basisCell - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
BasisCell(IMoleculeList, IVectorMutable) - Constructor for class etomica.normalmode.CoordinateDefinition.BasisCell
BasisCubicBcc - Class in etomica.lattice.crystal: A 2-atom basis for a bcc crystal
BasisCubicBcc() - Constructor for class etomica.lattice.crystal.BasisCubicBcc: Makes a bcc 2-atom basis.
BasisCubicDiamond - Class in etomica.lattice.crystal: An 8-atom basis that for a diamond crystal.
BasisCubicDiamond() - Constructor for class etomica.lattice.crystal.BasisCubicDiamond: Makes a diamond-on-fcc 8-atom basis.
BasisCubicFcc - Class in etomica.lattice.crystal: A 4-atom basis fot an fcc crystal.
BasisCubicFcc() - Constructor for class etomica.lattice.crystal.BasisCubicFcc: Makes a fcc 4-atom basis.
BasisCubicFccDiamond - Class in etomica.lattice.crystal: A 2-atom basis that makes a diamond crystal using a BravaisLattice having a Cubic primitive with an fcc basis.
BasisCubicFccDiamond() - Constructor for class etomica.lattice.crystal.BasisCubicFccDiamond: Makes a diamond-on-fcc 2-atom basis using the given factory to make the atoms.
basisDim - Variable in class etomica.normalmode.NormalModesMolecular
basisFCC - Variable in class etomica.normalmode.HessianDB
BasisHcp - Class in etomica.lattice.crystal: A 2-atom basis for an hcp crystal.
BasisHcp() - Constructor for class etomica.lattice.crystal.BasisHcp
BasisHcpBaseCentered - Class in etomica.lattice.crystal: A 2-atom basis for an hcp crystal (base-centered or side-centered)
BasisHcpBaseCentered() - Constructor for class etomica.lattice.crystal.BasisHcpBaseCentered
basisMolecules - Variable in class etomica.modules.sam.ConfigurationSAM
BasisMonatomic - Class in etomica.lattice.crystal: Single-atom basis with the coordinate at the origin.
BasisMonatomic(ISpace) - Constructor for class etomica.lattice.crystal.BasisMonatomic: Creates a single-atom basis with the coordinate at the origin.
BasisMonoclinicParacetamol - Class in etomica.paracetamol: An 4-atom basis that for a monoclinic paracetamol crystal.
BasisMonoclinicParacetamol() - Constructor for class etomica.paracetamol.BasisMonoclinicParacetamol: Makes a monoclinic-crystal paracetamol 4-atom basis.
basisOrientation - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
basisOrientation - Variable in class etomica.paracetamol.LatticeSumCrystalParacetamol
BasisOrthorhombicHexagonal - Class in etomica.lattice.crystal: A 2D hexagonal 2-atom basis
BasisOrthorhombicHexagonal() - Constructor for class etomica.lattice.crystal.BasisOrthorhombicHexagonal: Makes a 2D hexagonal 2-atom basis
BasisOrthorhombicHexagonal3D(ISpace) - Constructor for class etomica.modules.catalysis.ConfigurationCatalysis.BasisOrthorhombicHexagonal3D: Makes a fcc 4-atom basis.
BasisOrthorhombicParacetamol - Class in etomica.paracetamol: An 8-atom basis that for a orthorhombic paracetamol crystal.
BasisOrthorhombicParacetamol() - Constructor for class etomica.paracetamol.BasisOrthorhombicParacetamol: Makes a orthorhombic-crystal paracetamol 8-atom basis.
basisSize() - Method in class etomica.atom.iterator.ANIntergroupCoupled: Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ANIntergroupExchange: Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ANIntragroupExchange: Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ApiIndexList
basisSize() - Method in class etomica.atom.iterator.ApiIntergroup: Returns 2, indicating that the setBasis method expects an array of two atoms.
basisSize() - Method in class etomica.atom.iterator.ApiIntragroup: Returns 1, indicating the the array given to the setBasis method should have only one element.
basisSize() - Method in class etomica.atom.iterator.AtomIteratorBasis: Returns 1, indicating that only a single-atom basis is appropriate.
basisSize() - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart: Returns 1, indicating that only a single-atom basis is appropriate.
basisSize() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
basisSize() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
basisSize() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
basisSize() - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent: Indicates the size of the basis needed to set the iterator.
basisSize() - Method in interface etomica.atom.iterator.MoleculesetIteratorBasisDependent: Indicates the size of the basis needed to set the iterator.
basisSize() - Method in class etomica.atom.iterator.TripletInnerSequential
basisSize() - Method in class etomica.potential.PotentialMaster.AtomIterator0
basisSurface - Variable in class etomica.modules.sam.ConfigurationSAM
bB - Static variable in class etomica.models.co2.P2CO2Hellmann
bB - Static variable in class etomica.potential.P2NitrogenHellmann
BBbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
bBond - Variable in class etomica.virial.cluster.VirialDiagrams
bBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
bCalc(int) - Method in class etomica.veos.QSeries: Computes the coefficient b_j based on the beta coefficients given by the BetaSource.
BCC - Static variable in class etomica.normalmode.SoftSphereSolidEOS
BCC - Static variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
BCVisitor - Class in etomica.graph.traversal: This TraversalVisitor visits nodes and keeps track of biconnected components.
BCVisitor(List<List<Byte>>) - Constructor for class etomica.graph.traversal.BCVisitor
BDONE - Static variable in class etomica.virial.ClusterWheatleySoftBD
BDONE - Static variable in class etomica.virial.MeterVirialBDBin
bdrij - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
bdrij - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
bdry - Variable in class etomica.models.hexane.HexaneVolumeFraction
bdry - Variable in class etomica.models.hexane.SimHarmonicHexane
bdry - Variable in class etomica.models.hexane.TestHexane
bdry - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
bdry - Variable in class etomica.models.hexane.TestHexaneFileConfig
bdry - Variable in class etomica.models.hexane.TestHexaneHarmonic
bdry - Variable in class etomica.models.hexane.TestSetToUHexane
bdry - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
bdry - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
bdry - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
bdry - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
bdry - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
bdry - Variable in class etomica.models.oneDHardRods.SimWidomMode
bdry - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
bdry - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
bdry - Variable in class etomica.normalmode.SimCalcJ
bdry - Variable in class etomica.normalmode.SimCalcS
bdry - Variable in class etomica.normalmode.SimModesJ
bdry - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
bdry - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
bdry - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage
bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage
bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
BDZERO - Static variable in class etomica.virial.ClusterWheatleySoftBD
BDZERO - Static variable in class etomica.virial.MeterVirialBD
BDZERO - Static variable in class etomica.virial.MeterVirialBDBin
BDZERO - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
BDZERO - Static variable in class etomica.virial.MeterVirialSWWE
beadFac - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
beadFac - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
beadFac - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
beadFac - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
beadFac - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
beginRendering(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
beginRendering(Matrix3f) - Method in class org.jmol.util.GData
benBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
benBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
bennetUDiff - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
Bernoulli - Class in etomica.veos.bigdecimal: Bernoulli numbers.
Bernoulli() - Constructor for class etomica.veos.bigdecimal.Bernoulli
besselI(int, double) - Static method in class etomica.math.SpecialFunctions: Calculates the modified bessel function of the first kind (I) for a given order and the variable x.
beta - Variable in class etomica.mappedvirial.MappedUpotential
beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
beta - Variable in class etomica.models.hexane.MCMoveCBMC
beta - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
beta - Static variable in class etomica.potential.P1HydrogenMielke
beta - Variable in class etomica.potential.P4TorsionDreiding
beta - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
beta - Variable in class etomica.util.numerical.NonLinearCurveFitting
beta(int) - Method in interface etomica.veos.BetaSource
beta(int) - Method in class etomica.veos.HardRods
beta(int) - Method in class etomica.veos.VanderWaals
beta - Variable in class etomica.virial.ClusterChainSoft
beta - Variable in class etomica.virial.ClusterExchange
beta - Variable in class etomica.virial.ClusterSinglyConnected
beta - Variable in class etomica.virial.ClusterSum
beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
beta - Variable in class etomica.virial.ClusterTree
beta - Variable in class etomica.virial.ClusterWheatleyExtendSW
beta - Variable in class etomica.virial.ClusterWheatleyHS
beta - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
beta - Variable in class etomica.virial.ClusterWheatleySoft
beta - Variable in class etomica.virial.ClusterWheatleySoftBD
beta3 - Variable in class etomica.potential.P3CPSNonAdditiveHe
beta3 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
beta3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta3_111 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
beta3_112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta3_113 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta3_122 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta3_222 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHe
beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
beta4211_1112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta4211_1121 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta4211_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHe
beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
beta4220_1111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta4220_1211 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
beta4220_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
betaCoeffs - Variable in class etomica.models.nitrogen.FindTransitionTemperature
BetaPhaseLatticeParameter - Class in etomica.models.nitrogen: The parameters that are determined through conjugate gradient method to give the lowest lattice energy for beta-N2 phase structure
BetaPhaseLatticeParameter() - Constructor for class etomica.models.nitrogen.BetaPhaseLatticeParameter
BetaPhaseLatticeParameterLS - Class in etomica.models.nitrogen: The parameters that are determined through conjugate gradient method to give the lowest lattice energy for beta-N2 phase structure for lattice sum, rC = 250 A
BetaPhaseLatticeParameterLS() - Constructor for class etomica.models.nitrogen.BetaPhaseLatticeParameterLS
BetaPhaseLatticeParameterNA - Class in etomica.models.nitrogen: The parameters that are determined through conjugate gradient method to give the lowest lattice energy for beta-N2 phase structure
BetaPhaseLatticeParameterNA() - Constructor for class etomica.models.nitrogen.BetaPhaseLatticeParameterNA
BetaSource - Interface in etomica.veos
betaUAB - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
betaUAB - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
betaUAW - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
betaUAW - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
betaUAWf - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
betaUAWf - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
betaUBA - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
betaUBA - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
betaUBW - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
betaUBW - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
betaUBWf - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
betaUBWf - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
bgcolor - Variable in class org.jmol.util.GData
bGuess - Variable in class etomica.util.numerical.B9Optimizer
bGuess - Variable in class etomica.util.numerical.VirialOptimizer
BHS(int, double) - Static method in class etomica.virial.cluster.Standard: Returns the nth virial coefficient for hard spheres of diameter sigma.
BIAS - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
BIAS - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
bias - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
bias - Variable in class etomica.virial.MCMoveClusterTorsionMulti
biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolume
biasInsert(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeAceticAcid
biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeCube
biasInsert(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeMolecule
biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphere
biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOriented
biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
biasOld - Variable in class etomica.integrator.mcmove.MCMoveVolume
BiasVolume - Class in etomica.association
BiasVolume(ISpace) - Constructor for class etomica.association.BiasVolume
biasVolume() - Method in class etomica.association.BiasVolume
biasVolume() - Method in class etomica.association.BiasVolumeAceticAcid
biasVolume() - Method in class etomica.association.BiasVolumeCube
biasVolume() - Method in class etomica.association.BiasVolumeMolecule
biasVolume() - Method in class etomica.association.BiasVolumeSphere
biasVolume() - Method in class etomica.association.BiasVolumeSphereOriented
biasVolume() - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
BiasVolume2SiteAceticAcid - Class in etomica.association
BiasVolume2SiteAceticAcid(ISpace, IRandom) - Constructor for class etomica.association.BiasVolume2SiteAceticAcid
BiasVolumeAceticAcid - Class in etomica.association
BiasVolumeAceticAcid(ISpace, IRandom, IBox) - Constructor for class etomica.association.BiasVolumeAceticAcid
BiasVolumeCube - Class in etomica.association
BiasVolumeCube(ISpace, IRandom) - Constructor for class etomica.association.BiasVolumeCube
BiasVolumeMolecule - Class in etomica.association
BiasVolumeMolecule(ISpace) - Constructor for class etomica.association.BiasVolumeMolecule
BiasVolumeSphere - Class in etomica.association
BiasVolumeSphere(ISpace, IRandom) - Constructor for class etomica.association.BiasVolumeSphere
BiasVolumeSphereOriented - Class in etomica.association
BiasVolumeSphereOriented(ISpace, IRandom) - Constructor for class etomica.association.BiasVolumeSphereOriented
BiasVolumeSphereOrientedDoubleSites - Class in etomica.association
BiasVolumeSphereOrientedDoubleSites(ISpace, IRandom) - Constructor for class etomica.association.BiasVolumeSphereOrientedDoubleSites
BiComponentSubst - Class in etomica.graph.operations: This class handles the substitution g = A where g is a Graph and A is a set of Graph.
BiComponentSubst() - Constructor for class etomica.graph.operations.BiComponentSubst
BiComponentSubst.BiComponentSubstParameters - Class in etomica.graph.operations
BiComponentSubstParameters(Graph, Set<Graph>, boolean, boolean) - Constructor for class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
BiconectedNodalPoint - Class in etomica.graph.traversal
BiconectedNodalPoint() - Constructor for class etomica.graph.traversal.BiconectedNodalPoint
Biconnected - Class in etomica.graph.traversal
Biconnected() - Constructor for class etomica.graph.traversal.Biconnected
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHe
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeOrig
bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
BigComplex - Class in etomica.veos.bigdecimal: Complex numbers with BigDecimal real and imaginary components
BigComplex() - Constructor for class etomica.veos.bigdecimal.BigComplex: Default ctor equivalent to zero.
BigComplex(BigDecimal, BigDecimal) - Constructor for class etomica.veos.bigdecimal.BigComplex: ctor with real and imaginary parts
BigComplex(BigDecimal) - Constructor for class etomica.veos.bigdecimal.BigComplex: ctor with real part.
BigComplex(double, double) - Constructor for class etomica.veos.bigdecimal.BigComplex: ctor with real and imaginary parts
BigDecimalMath - Class in etomica.veos.bigdecimal: BigDecimal special functions.
BigDecimalMath() - Constructor for class etomica.veos.bigdecimal.BigDecimalMath
BigDecimalValue(MathContext) - Method in class etomica.veos.bigdecimal.BigSurd: Return the approximate floating point representation.
BigDecimalValue(MathContext) - Method in class etomica.veos.bigdecimal.BigSurdVec: Construct an approximate floating point representation
BigDecimalValue(MathContext) - Method in class etomica.veos.bigdecimal.Rational: Return a representation as BigDecimal.
BigIntegerMath - Class in etomica.veos.bigdecimal: BigInteger special functions and Number theory.
BigIntegerMath() - Constructor for class etomica.veos.bigdecimal.BigIntegerMath
BigIntegerPoly - Class in etomica.veos.bigdecimal: Polynomial with integer coefficients.
BigIntegerPoly() - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly: Default ctor.
BigIntegerPoly(String) - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly: Ctor with a comma-separated list as the list of coefficients.
BigIntegerPoly(Vector<BigInteger>) - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly: Ctor with a list of coefficients.
BigIntegerPoly(BigInteger[]) - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly: Ctor with a list of coefficients.
bigomega() - Method in class etomica.veos.bigdecimal.Ifactor: The sum of the prime factor exponents, with multiplicity.
BigSurd - Class in etomica.veos.bigdecimal: Square roots on the real line.
BigSurd() - Constructor for class etomica.veos.bigdecimal.BigSurd: Default ctor, which represents the zero.
BigSurd(Rational, Rational) - Constructor for class etomica.veos.bigdecimal.BigSurd: ctor given the prefactor and the basis of the root.
BigSurd(int, int) - Constructor for class etomica.veos.bigdecimal.BigSurd: ctor given the numerator and denominator of the root.
BigSurd(BigInteger) - Constructor for class etomica.veos.bigdecimal.BigSurd: ctor given the value under the root.
BigSurdVec - Class in etomica.veos.bigdecimal: A BigSurdVec represents an algebraic sum or differences of values which each term an instance of BigSurd.
BigSurdVec() - Constructor for class etomica.veos.bigdecimal.BigSurdVec: Default ctor, which represents the zero.
BigSurdVec(BigSurd) - Constructor for class etomica.veos.bigdecimal.BigSurdVec: ctor given the value of a BigSurd.
BigSurdVec(BigSurd, BigSurd) - Constructor for class etomica.veos.bigdecimal.BigSurdVec: ctor given two values, which (when added) represent this number a+b.
BigValue - Class in etomica.veos: Data class to handle operations involving large numbers.
BigValue() - Constructor for class etomica.veos.BigValue: Default constructor sets value to 0.0
BigValue(double) - Constructor for class etomica.veos.BigValue: Constructs using the given value.
BigValue(double, boolean) - Constructor for class etomica.veos.BigValue: Constructs given ln(|value|) and sign of value.
BigValue(IBigValue) - Constructor for class etomica.veos.BigValue: Copy constructor.
Binary - Interface in etomica.graph.operations
BINARY_OP_CONV - Static variable in interface etomica.graph.engine.Parser
BINARY_OP_DEL - Static variable in interface etomica.graph.engine.Parser
BINARY_OP_MUL - Static variable in interface etomica.graph.engine.Parser
BINARY_OP_SUB - Static variable in interface etomica.graph.engine.Parser
BINARY_OP_SUM - Static variable in interface etomica.graph.engine.Parser
BINARY_OP_UNION - Static variable in interface etomica.graph.engine.Parser
binaryExtensions - Static variable in class org.jmol.viewer.JmolConstants
BinaryOpByteImpl - Class in etomica.graph.engine.impl
BinaryOpByteImpl(String, Parser.Expression, Parser.Expression, byte) - Constructor for class etomica.graph.engine.impl.BinaryOpByteImpl
BinaryOpImpl - Class in etomica.graph.engine.impl
BinaryOpImpl(String, Parser.Expression, Parser.Expression) - Constructor for class etomica.graph.engine.impl.BinaryOpImpl
binom - Static variable in class etomica.math.SpecialFunctions
binom - Static variable in class etomica.potential.P2O2Bartolomei
binomial(int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate binomial(n,k).
binomial(BigInteger, BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate binomial(n,k).
binomial(Rational, BigInteger) - Static method in class etomica.veos.bigdecimal.Rational: binomial (n choose m).
binomial(Rational, int) - Static method in class etomica.veos.bigdecimal.Rational: binomial (n choose m).
binomialTInv(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Inverse Binomial transform.
binSize - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
binSize - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
binSize - Variable in class etomica.virial.MCMoveClusterTorsionMulti
bisectorVec - Static variable in class etomica.potential.P2WaterPotentialsJankowski
BishopPipin(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
BishopPipin(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
bitCount() - Method in interface etomica.graph.model.Bitmap: Returns the number of bits set in the bitmap.
bitCount() - Method in class etomica.graph.model.impl.AbstractBitmap
bitCount(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: Returns the number of valid bits in the long with the given index.
Bitmap - Interface in etomica.graph.model: Abstracts away the form in which bitmaps implement their operations and store their data.
BitmapFactory - Class in etomica.graph.model
BitmapFactory() - Constructor for class etomica.graph.model.BitmapFactory
BitmapOfLong - Class in etomica.graph.model.impl: This class encodes edges in a space efficient fashion, with the limitation that it can only encode up to 64 bits.
BitmapOfLong(Bitmap) - Constructor for class etomica.graph.model.impl.BitmapOfLong
BitmapOfLong(int) - Constructor for class etomica.graph.model.impl.BitmapOfLong
BitmapOfLong(int, boolean) - Constructor for class etomica.graph.model.impl.BitmapOfLong
BitmapOfLong(String) - Constructor for class etomica.graph.model.impl.BitmapOfLong
BitmapOfLong(byte[]) - Constructor for class etomica.graph.model.impl.BitmapOfLong
BitmapOfLong() - Constructor for class etomica.graph.model.impl.BitmapOfLong
BitmapOfLongVector - Class in etomica.graph.model.impl: Transparent implementation of arbitrarily large bitmaps based on an array of long values.
BitmapOfLongVector(Bitmap) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
BitmapOfLongVector(int) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
BitmapOfLongVector(int, boolean) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
BitmapOfLongVector(String) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
BitmapOfLongVector(byte[]) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
BitmapUtils - Class in etomica.graph.traversal
BitmapUtils() - Constructor for class etomica.graph.traversal.BitmapUtils
bitMask(byte) - Static method in class etomica.graph.traversal.BitmapUtils
bitOffMask(byte) - Static method in class etomica.graph.traversal.BitmapUtils
bitOffset(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit bitSize() - 1 of bitmap[size()-1].
bitOnMask(byte) - Static method in class etomica.graph.traversal.BitmapUtils
bitset - Static variable in class org.jmol.script.Token
BitSet - Class in org.jmol.util: a fast 64-bit BitSet optimized for Java2Script -- about 25 times faster than java.util.BitSet in JavaScript
BitSet() - Constructor for class org.jmol.util.BitSet: Creates a new bit set.
BitSetUtil - Class in org.jmol.util
BitSetUtil() - Constructor for class org.jmol.util.BitSetUtil
bitSize() - Method in interface etomica.graph.model.Bitmap: Returns the length in bits of the bitmap.
bitSize() - Method in class etomica.graph.model.impl.BitmapOfLong
bitSize() - Method in class etomica.graph.model.impl.BitmapOfLongVector
bl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
BLACK - Static variable in class org.jmol.util.Colix
blankPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
blMax - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
blN2 - Static variable in class etomica.potential.P2NitrogenHellmann
blN2 - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
blN2 - Static variable in class etomica.virial.simulations.VirialN2
blN2 - Static variable in class etomica.virial.simulations.VirialN2PI
blO2 - Static variable in class etomica.virial.simulations.VirialO2PI
BLOCK_CORRELATION - Static variable in class etomica.data.AccumulatorAverage
BLOCK_COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance
blockAccumulator - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
blockCorrelation - Variable in class etomica.data.AccumulatorAverage
blockCountDown - Variable in class etomica.data.AccumulatorAverage
blockCounter - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
blockCounter - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
blockCounter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
blockCovariance - Variable in class etomica.data.AccumulatorAverageCovariance
blockCovSum - Variable in class etomica.data.AccumulatorAverageCovariance
blockDataSink - Variable in class etomica.data.AccumulatorAverageFixed
blocks - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
blocks - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
blocks - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
blocks - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
blocksEq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
blocksEq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
blocksEq - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
blocksEq - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
blockSize - Variable in class etomica.data.AccumulatorAverage
blockSize - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
blockSize - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
blockSize - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
blockSize - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
blockSize - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
blockSize - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
blockSize - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
blockSize - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
blockSize - Variable in class etomica.virial.simulations.SimulationVirialOverlap
blockSize - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
blockSums - Variable in class etomica.data.AccumulatorAverageCollapsing
blockSums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
blOption - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
blOption - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
BLUE - Static variable in class org.jmol.util.Colix
bmu - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
bmu - Variable in class etomica.normalmode.DataSourceAvgPressure
bmu - Variable in class etomica.normalmode.DataSourceAvgPressure2
bmu - Variable in class etomica.normalmode.DataSourceFEHistogram
bmu - Variable in class etomica.normalmode.DataSourceImposedFEFit
bmu - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
bmu - Variable in class etomica.normalmode.DataSourceMuRoot
bmu - Variable in class etomica.normalmode.DataSourceMuRoot1
bmu - Variable in class etomica.normalmode.DataSourceMuRootPMatch
bmu - Variable in class etomica.normalmode.DataSourcePMu
bmuLat - Variable in class etomica.normalmode.DataSourceMuRoot
BnFlexibleContributionTraPPEUAMethanol - Class in etomica.virial.simulations: Computes (part of) the flexible contribution to the virial coefficient for the TraPPE-UA model of methanol (http://www.chem.umn.edu/groups/siepmann/trappe/intro.php) K.R.S.
BnFlexibleContributionTraPPEUAMethanol() - Constructor for class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
BnFlexibleContributionTraPPEUAMethanol.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
BnHNCLJ - Class in etomica.virial: This is just a main method for HypernettedChain.java...
BnHNCLJ() - Constructor for class etomica.virial.BnHNCLJ
BnHSIonic - Class in etomica.virial: ionic solution, restrictive primitive model (RPM) compute s, (phi[osmotic coefficient]-1) and ln(gamma) from HARD SPHERE interaction(from Standard class) 2nd ~ 5th order integrals are included p[] (<==> HSB[]) ==> integral = HSB[]* n! / (1-n) s[n] = c^n * HSB[n] / (1-n) ds[n]/dc = n * c ^ (n-1) * HSB[n] / (1-n) = s[n] * n/c cuz integral is independent of concentration in simulation units contains "linear step in sqrt(c)" && "linear step in c"
BnHSIonic() - Constructor for class etomica.virial.BnHSIonic
BnIETP2Spherical - Class in etomica.virial: This is just a main method for HypernettedChain.java or PercusYevick.java...
BnIETP2Spherical() - Constructor for class etomica.virial.BnIETP2Spherical
BnJHBVArgon_Analytic - Class in etomica.virial: Computes virial coefficients for argon using the analytical expressions developed by Jaeger, Hellmann, Bich, and Vogel (2011), JCP, 135: 084308.
BnJHBVArgon_Analytic() - Constructor for class etomica.virial.BnJHBVArgon_Analytic
BnPY_1QC_Helium - Class in etomica.virial: Computes the Percus-Yevick compressibility-route approximation for to the first quantum correction of Bn, where the first quantum correction is as defined Kim and Henderson (1968,1966).
BnPY_1QC_Helium() - Constructor for class etomica.virial.BnPY_1QC_Helium
BnPYCHe - Class in etomica.virial: This is just a main method for PercusYevick.java.
BnPYCHe() - Constructor for class etomica.virial.BnPYCHe
BnPYCHe.BnPYHeParams - Class in etomica.virial
BnPYHardSphere - Class in etomica.virial: This is just a main method for PercusYevick.java...
BnPYHardSphere() - Constructor for class etomica.virial.BnPYHardSphere
BnPYHeParams() - Constructor for class etomica.virial.BnPYCHe.BnPYHeParams
BnPYLJ - Class in etomica.virial: This is just a main method for PercusYevick.java.
BnPYLJ() - Constructor for class etomica.virial.BnPYLJ
BnSCALJ - Class in etomica.virial: Combines the Percus-Yevick and hypernetted-chain approximations to the virial coefficients to generate a self-consistent (thermodynamically consistent) approximation.
BnSCALJ() - Constructor for class etomica.virial.BnSCALJ
bohrConv - Variable in class etomica.models.water.P2WaterSzalewicz
BohrRadius - Class in etomica.units: The Borh Radius unit of length, corresponding to the size of a Hydrogen atom's electron cloud.
BOLTZMANN_K - Static variable in class etomica.util.Constants: Boltzmann's constant, in (sim units)/kelvin.
boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
BoltzmannProcessor - Class in etomica.normalmode: DataProcessor that returns the Boltzmann factor of the incoming energy.
BoltzmannProcessor() - Constructor for class etomica.normalmode.BoltzmannProcessor
bond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: this function will bond atoms a & b together
bond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: this function will bond atoms a & b together
bond - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
bond - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
Bond - Class in g3dsys.images
Bond(G3DSys, Ball, Ball) - Constructor for class g3dsys.images.Bond
Bond(G3DSys, Ball, Ball, short) - Constructor for class g3dsys.images.Bond
BOND_ORDER_MAP - Static variable in interface etomica.graph.model.Metadata
BONDAC - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
BONDAC - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
BondArrayList() - Constructor for class etomica.potential.P2HardBondedList.BondArrayList
BONDBC - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
BONDBC - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
BONDCA - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
BONDCA - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
BONDCB - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
BONDCB - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
BondChangeData() - Constructor for class etomica.potential.PotentialReactive.BondChangeData
BondConnectedSubstitution - Class in etomica.virial.cluster: If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitution() - Constructor for class etomica.virial.cluster.BondConnectedSubstitution
BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site - Class in etomica.virial.cluster
BondConnectedSubstitution3Site - Class in etomica.virial.cluster: If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitution3Site() - Constructor for class etomica.virial.cluster.BondConnectedSubstitution3Site
BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site - Class in etomica.virial.cluster
BondConnectedSubstitutionNaphthalene - Class in etomica.virial.cluster: revised from Hye Min's "BondConnectedSubstitution" If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
BondConnectedSubstitutionNaphthalene() - Constructor for class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa - Class in etomica.virial.cluster
BondConnectedSubstitutionParameters2Site(char, char) - Constructor for class etomica.virial.cluster.BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
BondConnectedSubstitutionParameters2SiteNa(char, char, List<Character>, List<Character>, List<Character>, List<Character>) - Constructor for class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
BondConnectedSubstitutionParameters3Site(char, char) - Constructor for class etomica.virial.cluster.BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
BondConstraints(int[][], double[]) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
bondCount - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
bondcount - Static variable in class org.jmol.script.Token
bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
bondDecomp - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
bondDecomp - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
bondedAtom1 - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
bondedAtom2 - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
bondedAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
bondedAtoms - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
bondedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
bondedSet - Variable in class etomica.modules.render.RenderMD.CriterionCar
bondFac - Variable in class etomica.modules.colloid.P2HardSphereMC
bondFac - Variable in class etomica.modules.colloid.P2SquareWellMonomer
bondIndexArray - Variable in class etomica.virial.ClusterBonds
BondInfo(int, int, double) - Constructor for class etomica.modules.render.ParseObj.BondInfo
bondingAgentManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
bondingAngleRestriction - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
bondingAngleRestriction - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
bondingAngleRestriction - Variable in class etomica.models.water.PNWaterGCPMThreeSite
bondingPotential - Variable in class etomica.chem.models.ModelChain
BondInteractionTypeToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.BondInteractionTypeToggler
bondIteratorsHash - Variable in class etomica.graphics.BondListener
bondL - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
bondL - Variable in class etomica.virial.Conformation7SiteRigidSF6
bondL - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
bondL - Variable in class etomica.virial.SpeciesFactorySpheres2
bondL_CC - Variable in class etomica.modules.sam.Sam
bondLength - Variable in class etomica.atom.AtomHydrogen
bondLength - Variable in class etomica.config.ConformationLinear
bondlength - Variable in class etomica.models.hexane.CBMCGrowStraightAlkane
bondlength - Static variable in class etomica.virial.ConformationAnthracene3site
bondlength - Static variable in class etomica.virial.ConformationCO2
bondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
bondlength - Static variable in class etomica.virial.ConformationPh3site
bondLength - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
bondLength - Variable in class etomica.virial.MCMoveClusterTorsionMulti
bondLengthOH - Static variable in class etomica.models.water.ConformationWater3P
bondLengthOH - Static variable in class etomica.models.water.ConformationWaterTIP4P
bondLengths - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
bondList - Variable in class etomica.association.MCMoveAtomSmer
bondList - Variable in class etomica.association.MCMoveMoleculeSmer
bondList - Variable in class etomica.modules.render.ParseObj
bondList - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
BondListener - Class in etomica.graphics: BondListener listens for Atoms being added to the Simulation, determines what covalent bonds (if any) apply to the new Atom and informs a BondManager of any new bonds.
BondListener(IBox, BondManager) - Constructor for class etomica.graphics.BondListener: Creates a new BondListener for the given Box, using the given BondManager to actually create or remove bonds.
bondManager - Variable in class etomica.graphics.BondListener
BondManager - Interface in etomica.graphics: The BondManager is responsible for creation and disposal of bonds between atom pairs.
bondManager - Variable in class etomica.modules.colloid.P2HardSphereMC
bondManager - Variable in class etomica.modules.colloid.P2SquareWellMonomer
bondManager - Variable in class etomica.modules.sam.CriterionTether3
bondMap - Variable in class etomica.graph.operations.ExcludeParameters
bondMap - Variable in class etomica.modules.render.RenderMD.P2PenetrableCar
bondmodeor - Static variable in class org.jmol.script.Token
bondOrigN - Static variable in class etomica.models.nitrogen.ConformationNitrogen
bondOrigN - Static variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
bondOrigP - Static variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
bondOrigP1 - Static variable in class etomica.models.nitrogen.ConformationNitrogen
bondOrigP2 - Static variable in class etomica.models.nitrogen.ConformationNitrogen
bondpicking - Static variable in class org.jmol.script.Token
bondradiusmilliangstroms - Static variable in class org.jmol.script.Token
bonds - Variable in class etomica.virial.MCMoveClusterAtomHSTree
bonds - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
bonds - Static variable in class org.jmol.script.Token
bondsA - Variable in class etomica.graph.operations.CombineABSite.CombineABSiteParameters
bondsB - Variable in class etomica.graph.operations.CombineABSite.CombineABSiteParameters
bondsTree - Variable in class etomica.virial.ClusterTree
bondTheta - Variable in class etomica.modules.sam.Sam
bondTheta - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
bondTheta - Variable in class etomica.virial.SpeciesFactorySpheres2
bondtolerance - Static variable in class org.jmol.script.Token
bondType - Variable in class etomica.models.OPLS.P2AceticAcidTwoSite
bondTypeToggler - Variable in class etomica.modules.clustergenerator.MyApplet
BondTypeToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.BondTypeToggler
booleanparam - Static variable in class org.jmol.script.Token
bootstrap() - Method in class etomica.graph.iterators.CartesianIterator
bootstrap() - Method in class etomica.graph.iterators.CartesianPermutator
BORDER - Static variable in class etomica.graphics.DeviceBox.LabelType
BORDER - Static variable in class etomica.graphics.DisplayTextBox.LabelType
BOT - Static variable in class etomica.math.Gamma
BOTEXP - Static variable in class etomica.math.Gamma
bothSides - Variable in class etomica.modules.adsorption.MyMCMove
BOTTOM - Static variable in class etomica.graphics.DisplayBox
BOTTOM - Static variable in class etomica.graphics.DisplayPolytope
BOTTOM - Static variable in class etomica.util.Constants.Direction
boundaries - Variable in class etomica.modules.rosmosis.MeterFlux
boundary - Variable in class etomica.association.AssociationHelperBranched
boundary - Variable in class etomica.association.AssociationHelperDouble
boundary - Variable in class etomica.association.AssociationHelperMolecule
boundary - Variable in class etomica.atom.AtomPositionGeometricCenterPBC
boundary - Variable in class etomica.data.meter.PotentialCalculationRDF
boundary - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
boundary - Variable in class etomica.graphics.ColorSchemeOverlap
boundary - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
boundary - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
boundary - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
boundary - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
boundary - Variable in class etomica.meam.PotentialCuLREP
boundary - Variable in class etomica.meam.PotentialEFS
boundary - Variable in class etomica.meam.PotentialFeEAM
boundary - Variable in class etomica.meam.PotentialFeEAM_LS
boundary - Variable in class etomica.meam.PotentialMEAM
boundary - Variable in class etomica.models.co2.PNCO2GCPM
boundary - Variable in class etomica.models.co2.PNGCPM
boundary - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
boundary - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
boundary - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
boundary - Variable in class etomica.models.nitrogen.P2Nitrogen
boundary - Variable in class etomica.models.nitrogen.P2NitrogenAB
boundary - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
boundary - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
boundary - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
boundary - Variable in class etomica.models.water.P2Water3P
boundary - Variable in class etomica.models.water.P2Water4P
boundary - Variable in class etomica.models.water.P2WaterTIP4PHardCore
boundary - Variable in class etomica.models.water.PNWaterGCPM
boundary - Variable in class etomica.models.water.TestEwaldTIP4PWater
boundary - Variable in class etomica.modules.adsorption.P1Wall
boundary - Variable in class etomica.modules.colloid.P1Wall
boundary - Variable in class etomica.modules.interfacial.MeterOrientation
boundary - Variable in class etomica.nbr.CriterionSimple
boundary - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
boundary - Variable in class etomica.normalmode.HessianDB
boundary - Variable in class etomica.normalmode.LJVacancyMin
boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
boundary - Variable in class etomica.normalmode.NormalModes1DHR
boundary - Variable in class etomica.normalmode.NormalModes2D
boundary - Variable in class etomica.normalmode.P1ConstraintNbr
boundary - Variable in class etomica.normalmode.P1ConstraintNbrHcp
boundary - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
boundary - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
boundary - Variable in class etomica.normalmode.SimBennet
boundary - Variable in class etomica.normalmode.SimCalcSLJ
boundary - Variable in class etomica.normalmode.SimCalcSMorse
boundary - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
boundary - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
boundary - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
boundary - Variable in class etomica.normalmode.SimEinStep1
boundary - Variable in class etomica.normalmode.SimEinStep1HCP
boundary - Variable in class etomica.normalmode.SimEinStep2
boundary - Variable in class etomica.normalmode.SimEinStep2HCP
boundary - Variable in class etomica.normalmode.SimHarmonic
boundary - Variable in class etomica.normalmode.SimHarmonicUmbrella
boundary - Variable in class etomica.normalmode.SimLJHTTISuper
boundary - Variable in class etomica.normalmode.SimLJHTTISuperHCP
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
boundary - Variable in class etomica.normalmode.SimTarget
boundary - Variable in class etomica.normalmode.SimTargetUmbrella
boundary - Variable in class etomica.normalmode.SimUmbrella
boundary - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
boundary - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
boundary - Variable in class etomica.potential.P1HardBoundary
boundary - Variable in class etomica.potential.P1HydrogenMielke
boundary - Variable in class etomica.potential.P2CO2EMP
boundary - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
boundary - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
boundary - Variable in class etomica.potential.P2HydrogenHinde
boundary - Variable in class etomica.potential.P2HydrogenHindeAtomic
boundary - Variable in class etomica.potential.P2HydrogenHindePatkowski
boundary - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
boundary - Variable in class etomica.potential.P2HydrogenPatkowski
boundary - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
boundary - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
boundary - Variable in class etomica.potential.P2MoleculeTruncated
boundary - Variable in class etomica.potential.P2NitrogenHellmann
boundary - Variable in class etomica.potential.P2O2Bartolomei
boundary - Variable in class etomica.potential.P2QChem
boundary - Variable in class etomica.potential.P2ReactionFieldDipole
boundary - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
boundary - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
boundary - Variable in class etomica.potential.P2SoftTruncated
boundary - Variable in class etomica.potential.P2SpheroPolyhedron
boundary - Variable in class etomica.potential.P2WaterPotentialsJankowski
boundary - Variable in class etomica.potential.P3AxilrodTeller
boundary - Variable in class etomica.potential.P3BondAngle
boundary - Variable in class etomica.potential.P3BondAngleDreiding
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHe
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
boundary - Variable in class etomica.potential.P3HydrogenATM
boundary - Variable in class etomica.potential.P3HydrogenManzhos
boundary - Variable in class etomica.potential.P3Induction
boundary - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
boundary - Variable in class etomica.potential.P4BondTorsion
boundary - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
boundary - Variable in class etomica.potential.P4TorsionDreiding
boundary - Variable in class etomica.potential.Potential1
boundary - Variable in class etomica.potential.Potential2HardSpherical
boundary - Variable in class etomica.potential.Potential2SoftSpherical
boundary - Variable in class etomica.potential.Potential2SoftSphericalLS
boundary - Variable in class etomica.potential.PotentialEmul
Boundary - Class in etomica.space: Parent class of boundary objects that describe the size and periodic nature of the box boundaries.
Boundary(ISpace, Polytope) - Constructor for class etomica.space.Boundary: Subclasses must invoke this constructor and provide a Space instance that can be used to generate Vectors, and a Polytope that defines the shape and volume of the boundary region.
boundary - Variable in class etomica.space.BoundaryEvent
boundaryCoefficients - Variable in class etomica.modules.rosmosis.MeterFlux
BoundaryDeformableLattice - Class in etomica.space: Deformable boundary that takes the shape of a primitive with some number of cells in each dimension.
BoundaryDeformableLattice(Primitive, int[]) - Constructor for class etomica.space.BoundaryDeformableLattice: Creates boundary with the shape of the given primitive and the given number of cells for each dimension.
BoundaryDeformableLattice(Primitive, double[]) - Constructor for class etomica.space.BoundaryDeformableLattice: Creates boundary with the shape of the given primitive and the given number of cells for each dimension.
BoundaryDeformablePeriodic - Class in etomica.space: Boundary shaped as an arbitrary parallelepiped.
BoundaryDeformablePeriodic(ISpace) - Constructor for class etomica.space.BoundaryDeformablePeriodic: Make a cubic boundary with edges of length equal to the default boxSize and periodic in every direction.
BoundaryDeformablePeriodic(ISpace, double) - Constructor for class etomica.space.BoundaryDeformablePeriodic: Make a cubic boundary of specified edge length and periodicity.
BoundaryDeformablePeriodic(ISpace, IVector[]) - Constructor for class etomica.space.BoundaryDeformablePeriodic: Make a parallelepiped boundary of specified shape and periodicity.
BoundaryDeformablePeriodicSwitch - Class in etomica.models.nitrogen
BoundaryDeformablePeriodicSwitch(ISpace, IVector[]) - Constructor for class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
BoundaryEvent - Class in etomica.space
BoundaryEvent(IBoundary) - Constructor for class etomica.space.BoundaryEvent
BoundaryEventManager - Class in etomica.space
BoundaryEventManager() - Constructor for class etomica.space.BoundaryEventManager
boundaryHardA - Variable in class etomica.modules.osmosis.OsmosisSim
boundaryHardB - Variable in class etomica.modules.osmosis.OsmosisSim
boundaryHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
boundaryHarmonic - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlap
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapLJ
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapLJModule
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphere
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSSnxy
boundaryInflate(IBoundaryEvent) - Method in interface etomica.api.IBoundaryListener
boundaryInflate(IBoundaryEvent) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
boundaryInflate(IBoundaryEvent) - Method in class etomica.nbr.cell.NeighborCellManager
boundaryPadding - Variable in class etomica.config.ConfigurationLattice
BoundaryPistonCylinder - Class in etomica.modules.pistoncylinder: Boundary class for PistonCylinder that accounts for the piston and collision radius when calculating the (available) volume
BoundaryPistonCylinder(ISpace) - Constructor for class etomica.modules.pistoncylinder.BoundaryPistonCylinder
BoundaryRectangular - Class in etomica.space: Boundary that is in the shape of a rectangular parallelepiped.
BoundaryRectangular(ISpace) - Constructor for class etomica.space.BoundaryRectangular: Constructs cubic boundary of the given periodicity, using the space and default box-size given by the Simulation.
BoundaryRectangular(ISpace, double) - Constructor for class etomica.space.BoundaryRectangular: Constructs cubic boundary of the given periodicity with each edge of length boxSize
BoundaryRectangular(ISpace, double[]) - Constructor for class etomica.space.BoundaryRectangular: Constructs rectangular boundary of the given periodicity with edges given by the values in the array boxSize.
BoundaryRectangularNonperiodic - Class in etomica.space: Boundary that is not periodic in any direction.
BoundaryRectangularNonperiodic(ISpace) - Constructor for class etomica.space.BoundaryRectangularNonperiodic: Make a boundary with unit volume.
BoundaryRectangularPeriodic - Class in etomica.space: Rectangular boundary that is periodic in every dimension.
BoundaryRectangularPeriodic(ISpace) - Constructor for class etomica.space.BoundaryRectangularPeriodic: Constructs cubic boundary with the default box-size given by the Simulation.
BoundaryRectangularPeriodic(ISpace, double) - Constructor for class etomica.space.BoundaryRectangularPeriodic: Constructs cubic boundary for the given Space, with each edge of length boxSize.
BoundaryRectangularPeriodic(ISpace, double[]) - Constructor for class etomica.space.BoundaryRectangularPeriodic: Constructs rectangular boundary for the given Space, with each edge of length boxSize.
BoundaryRectangularPeriodicSwitch - Class in etomica.models.nitrogen
BoundaryRectangularPeriodicSwitch(ISpace) - Constructor for class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
BoundaryRectangularPore - Class in etomica.space: Class for implementing pore periodic boundary conditions, in which one dimension is periodic.
BoundaryRectangularPore(ISpace) - Constructor for class etomica.space.BoundaryRectangularPore: Makes cubic volume with the x-dimension (index 0) not periodic.
BoundaryRectangularPore(ISpace, int) - Constructor for class etomica.space.BoundaryRectangularPore: Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularPore(ISpace, int, double) - Constructor for class etomica.space.BoundaryRectangularPore: Constructor for periodic boundary conditions with a pore in the given dimension.
BoundaryRectangularSlit - Class in etomica.space: Class for implementing slit periodic boundary conditions, in which one dimension is not periodic.
BoundaryRectangularSlit(ISpace) - Constructor for class etomica.space.BoundaryRectangularSlit: Makes cubic volume with the x-dimension (index 0) not periodic.
BoundaryRectangularSlit(int, ISpace) - Constructor for class etomica.space.BoundaryRectangularSlit: Makes cubic volume with the indicated dimension not periodic.
BoundaryRectangularSlit(int, double, ISpace) - Constructor for class etomica.space.BoundaryRectangularSlit: Constructor for periodic boundary conditions with a slit in the given dimension.
boundaryRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
boundaryRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
boundaryRef - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
boundaryRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
boundarySemiB - Variable in class etomica.modules.osmosis.OsmosisSim
boundaryTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
boundaryTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
boundaryTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
boundaryTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
boundaryTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
boundaryTarget - Variable in class etomica.normalmode.SimOverlap
boundaryTarget - Variable in class etomica.normalmode.SimOverlapLJ
boundaryTarget - Variable in class etomica.normalmode.SimOverlapLJModule
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
boundaryTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
BoundaryTruncatedOctahedron - Class in etomica.space3d: This class enables creation of a periodic truncated-octahedron boundary.
BoundaryTruncatedOctahedron(ISpace) - Constructor for class etomica.space3d.BoundaryTruncatedOctahedron
BoundaryTruncatedOctahedron(ISpace, double) - Constructor for class etomica.space3d.BoundaryTruncatedOctahedron
boundbox - Static variable in class org.jmol.script.Token
boundboxcolor - Static variable in class org.jmol.script.Token
box - Variable in class etomica.action.BoxActionAdapter
box - Variable in class etomica.action.BoxRandomizeMomenta
box - Variable in class etomica.action.BoxScaleMomenta
box - Variable in class etomica.action.WriteConfiguration
box - Variable in class etomica.AlkaneEH.CH4NVT
box - Variable in class etomica.AlkaneEH.DHS_NVT
box - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
box - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
box - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
box - Variable in class etomica.association.TestLJAssociationMC3D_NPT
box - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
box - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
box - Variable in class etomica.atom.AtomLeafAgentManager
box - Variable in class etomica.atom.AtomSourceRandomSpecies
box - Variable in class etomica.atom.iterator.MoleculeIteratorAll
box - Variable in class etomica.atom.iterator.MpiIntraspecies1A
box - Variable in class etomica.atom.MoleculeAgentManager
box - Variable in class etomica.atom.MoleculeSourceRandomMolecule
Box - Class in etomica.box: A Box collects all atoms that interact with one another; atoms in different boxs do not interact.
Box(ISpace) - Constructor for class etomica.box.Box: Constructs box with default rectangular periodic boundary.
Box(IBoundary, ISpace) - Constructor for class etomica.box.Box: Constructs box with the given boundary
box - Variable in class etomica.box.BoxEvent
box - Variable in class etomica.box.RandomPositionSourceDeformable
box - Variable in class etomica.box.RandomPositionSourceRectangular
box - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
box - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
box - Variable in class etomica.data.DataProcessorInterfacialTension
box - Variable in class etomica.data.meter.MeterDihedralAngle
box - Variable in class etomica.data.meter.MeterHyperVirial
box - Variable in class etomica.data.meter.MeterKineticEnergyRigid
box - Variable in class etomica.data.meter.MeterPotentialEnergy
box - Variable in class etomica.data.meter.MeterPressure
box - Variable in class etomica.data.meter.MeterPressureTensor
box - Variable in class etomica.data.meter.MeterProfileByAtoms
box - Variable in class etomica.data.meter.MeterProfileByVolume
box - Variable in class etomica.data.meter.MeterRDF
box - Variable in class etomica.data.meter.MeterRDFPC
box - Variable in class etomica.data.meter.MeterStructureFactor
box - Variable in class etomica.data.meter.MeterTemperature
box - Variable in class etomica.data.meter.MeterWidomInsertion
box - Variable in class etomica.densityofstate.DensityOfState
box - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
box - Variable in class etomica.dielectric.DHS_NVT
box - Variable in class etomica.dielectric.DLJ_NVT_1site
box - Variable in class etomica.dielectric.TIP4P_NVT
box - Variable in class etomica.dimer.EnergyMap
box - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
box - Variable in class etomica.dimer.SimDimerLJadatom
box - Variable in class etomica.dimer.SimDimerLJgb
box - Variable in class etomica.dimer.SimDimerMEAMadatom
box - Variable in class etomica.dimer.SimDimerMEAMGB
box - Variable in exception etomica.exception.ConfigurationOverlapException
box - Variable in class etomica.freeenergy.npath.DataSourceEnergies
box - Variable in class etomica.freeenergy.npath.SimIdealGas
box - Variable in class etomica.freeenergy.npath.SimLJ
box - Variable in class etomica.graphics.BondListener
box - Variable in class etomica.graphics.DeviceNSelector
box - Variable in class etomica.integrator.IntegratorBox
box - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
box - Variable in class etomica.integrator.mcmove.MCMoveBox
box - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
box - Variable in class etomica.interfacial.FixedWall
box - Variable in class etomica.interfacial.LJMC
box - Variable in class etomica.interfacial.LJMD
box - Variable in class etomica.interfacial.MeterWallForce
box - Variable in class etomica.interfacial.MeterWallPosition
box - Variable in class etomica.kmc.SimKMCLJadatom
box - Variable in class etomica.kmc.SimKMCMEAMadatom
box - Variable in class etomica.liquidLJ.DataProcessorReweight
box - Variable in class etomica.liquidLJ.LjMC3D
box - Variable in class etomica.liquidLJ.LjMd3D
box - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
box - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
box - Variable in class etomica.liquidLJ.MeterPU
box - Variable in class etomica.liquidLJ.MeterPUCut
box - Variable in class etomica.liquidLJ.MeterPUCutLS
box - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
box - Variable in class etomica.liquidLJ.MeterWidomInsertionP
box - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
box - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
box - Variable in class etomica.mappedvirial.MappedU
box - Variable in class etomica.mappedvirial.MappedUpotential
box - Variable in class etomica.mappedvirial.MappedVirialLJ
box - Variable in class etomica.mappedvirial.MappedVirialLJVGr
box - Variable in class etomica.mappedvirial.MeterMappedU
box - Variable in class etomica.mappedvirial.MeterMappedVirial
box - Variable in class etomica.mappedvirial.MeterMappedVirialV
box - Variable in class etomica.mappedvirial.MeterMeanForce
box - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
box - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
box - Variable in class etomica.meam.EFSTungsten
box - Variable in class etomica.meam.MEAM_3DMDwithGB
box - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
box - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
box - Variable in class etomica.meam.MEAM_MC
box - Variable in class etomica.meam.MEAMMd3D
box - Variable in class etomica.metastable.LJmuVT
box - Variable in class etomica.metastable.LJNPT
box - Variable in class etomica.metastable.LJNVT
box - Variable in class etomica.metastable.MeterDensityDistribution
box - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
box - Variable in class etomica.models.clathrates.MinimizationTIP4P
box - Variable in class etomica.models.hexane.HexaneVolumeFraction
box - Variable in class etomica.models.hexane.SimHarmonicHexane
box - Variable in class etomica.models.hexane.TestHexane
box - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
box - Variable in class etomica.models.hexane.TestHexaneFileConfig
box - Variable in class etomica.models.hexane.TestHexaneHarmonic
box - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
box - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
box - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
box - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
box - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
box - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
box - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
box - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
box - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
box - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
box - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
box - Variable in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
box - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
box - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
box - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
box - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
box - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
box - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
box - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
box - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
box - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
box - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
box - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
box - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
box - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
box - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
box - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
box - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
box - Variable in class etomica.models.oneDHardRods.SimWidomMode
box - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
box - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
box - Variable in class etomica.models.rowley.DimerApproach
box - Variable in class etomica.models.water.TestEwaldTIP4PWater
box - Variable in class etomica.modifier.ModifierNMolecule
box - Variable in class etomica.modules.adsorption.Adsorption
box - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
box - Variable in class etomica.modules.catalysis.Catalysis
box - Variable in class etomica.modules.catalysis.MeterDensityCO
box - Variable in class etomica.modules.catalysis.MeterDensityCO2
box - Variable in class etomica.modules.catalysis.MeterDensityO2
box - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
box - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
box - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
box - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
box - Variable in class etomica.modules.chainequilibrium.MeterChainLength
box - Variable in class etomica.modules.chainequilibrium.MeterConversion
box - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
box - Variable in class etomica.modules.colloid.ColloidSim
box - Variable in class etomica.modules.colloid.MeterEnd2End
box - Variable in class etomica.modules.crystalviewer.CrystalViewer
box - Variable in class etomica.modules.crystalviewer.LatticeEditor
box - Variable in class etomica.modules.dcvgcmd.DCVGCMD
box - Variable in class etomica.modules.droplet.Droplet
box - Variable in class etomica.modules.droplet.DropletAtomic
box - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
box - Variable in class etomica.modules.droplet.MeterDeformation
box - Variable in class etomica.modules.ensembles.LJMC
box - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
box - Variable in class etomica.modules.entropylottery.EntropyLottery
box - Variable in class etomica.modules.entropylottery.MeterEntropy
box - Variable in class etomica.modules.insertion.Insertion
box - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
box - Variable in class etomica.modules.interfacial.InterfacialSW
box - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
box - Variable in class etomica.modules.ljmd.Ljmd
box - Variable in class etomica.modules.materialfracture.MaterialFracture
box - Variable in class etomica.modules.materialfracture.MeterElongation
box - Variable in class etomica.modules.materialfracture.MeterLoad
box - Variable in class etomica.modules.materialfracture.MeterStrain
box - Variable in class etomica.modules.materialfracture.MeterStress
box - Variable in class etomica.modules.materialfracture.P1Tension
box - Variable in class etomica.modules.materialfracture.StrainColorScheme
box - Variable in class etomica.modules.mu.MeterDensitySides
box - Variable in class etomica.modules.mu.Mu
box - Variable in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
box - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
box - Variable in class etomica.modules.osmosis.OsmosisSim
box - Variable in class etomica.modules.pistoncylinder.PistonCylinder
box - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
box - Variable in class etomica.modules.render.RenderMD: The Box holding the atoms.
box - Variable in class etomica.modules.rheology.MeterEndToEnd
box - Variable in class etomica.modules.rheology.MeterNormalStress
box - Variable in class etomica.modules.rheology.MeterViscosity
box - Variable in class etomica.modules.rheology.SimulationRheology
box - Variable in class etomica.modules.rosmosis.MeterFlux
box - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
box - Variable in class etomica.modules.rosmosis.ReverseOsmosis
box - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
box - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
box - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
box - Variable in class etomica.modules.sam.CriterionTether3
box - Variable in class etomica.modules.sam.MeterTilt
box - Variable in class etomica.modules.sam.MeterWallPressure
box - Variable in class etomica.modules.sam.Sam
box - Variable in class etomica.modules.swmd.Swmd
box - Variable in class etomica.modules.vle.MeterPressure2
box - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
box - Variable in class etomica.nbr.cell.NeighborCellManager
box - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
box - Variable in class etomica.nbr.list.NeighborListManager
box - Variable in class etomica.normalmode.CoordinateDefinition
box - Variable in class etomica.normalmode.DeviceCellNum3DSlider
box - Variable in class etomica.normalmode.DeviceCellNumXYSlider
box - Variable in class etomica.normalmode.HessianDB
box - Variable in class etomica.normalmode.HSDimerNPT
box - Variable in class etomica.normalmode.HSNPT
box - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
box - Variable in class etomica.normalmode.LJVacancyMin
box - Variable in class etomica.normalmode.MeterAPIPotentialEnergy
box - Variable in class etomica.normalmode.MeterMaxExpansion
box - Variable in class etomica.normalmode.MeterPhiDeviation
box - Variable in class etomica.normalmode.MeterPlaneSlip
box - Variable in class etomica.normalmode.MeterSolidDA
box - Variable in class etomica.normalmode.MeterSolidDACut
box - Variable in class etomica.normalmode.MeterSolidMirror
box - Variable in class etomica.normalmode.MeterThetaDeviation
box - Variable in class etomica.normalmode.MeterTilt
box - Variable in class etomica.normalmode.MeterTiltHistogram
box - Variable in class etomica.normalmode.MeterTiltRotation
box - Variable in class etomica.normalmode.MeterTiltRotationHistogram
box - Variable in class etomica.normalmode.MeterTiltRotationStdev
box - Variable in class etomica.normalmode.MinimizeHCP
box - Variable in class etomica.normalmode.ModifierCells3D
box - Variable in class etomica.normalmode.ModifierXCells2D
box - Variable in class etomica.normalmode.ModifierYCells2D
box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
box - Variable in class etomica.normalmode.NormalModesMolecular
box - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
box - Variable in class etomica.normalmode.P2XOrder
box - Variable in class etomica.normalmode.PotentialCalculationEFSSP
box - Variable in class etomica.normalmode.PotentialCalculationLJSP
box - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
box - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
box - Variable in class etomica.normalmode.SimBennet
box - Variable in class etomica.normalmode.SimCalcJ
box - Variable in class etomica.normalmode.SimCalcS
box - Variable in class etomica.normalmode.SimCalcSLJ
box - Variable in class etomica.normalmode.SimCalcSMorse
box - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
box - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
box - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
box - Variable in class etomica.normalmode.SimEinStep1
box - Variable in class etomica.normalmode.SimEinStep1HCP
box - Variable in class etomica.normalmode.SimEinStep2
box - Variable in class etomica.normalmode.SimEinStep2HCP
box - Variable in class etomica.normalmode.SimFluidSoftSphere
box - Variable in class etomica.normalmode.SimHarmonic
box - Variable in class etomica.normalmode.SimHarmonicUmbrella
box - Variable in class etomica.normalmode.SimHSMDVacancy
box - Variable in class etomica.normalmode.SimLJHTTISuper
box - Variable in class etomica.normalmode.SimLJHTTISuperHCP
box - Variable in class etomica.normalmode.SimLJVacancy
box - Variable in class etomica.normalmode.SimModesJ
box - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
box - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
box - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
box - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
box - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
box - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
box - Variable in class etomica.normalmode.SimTarget
box - Variable in class etomica.normalmode.SimTargetUmbrella
box - Variable in class etomica.normalmode.SimUmbrella
box - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
box - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
box - Variable in class etomica.paracetamol.MDParacetamolMonoclinic: The Box holding the atoms.
box - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic: The Box holding the atoms.
box - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
box - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
box - Variable in class etomica.potential.EwaldSummation
box - Variable in class etomica.potential.EwaldSumMolecules
box - Variable in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
box - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
box - Variable in class etomica.potential.Potential0Lrc
box - Variable in class etomica.potential.PotentialGroup
box - Variable in class etomica.rotation.DipoleBox
box - Variable in class etomica.rotation.DipoleBoxMatrix
box - Variable in class etomica.simulation.prototypes.ChainHSMD3D
box - Variable in class etomica.simulation.prototypes.HsMc2d
box - Variable in class etomica.simulation.prototypes.HSMD2D
box - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
box - Variable in class etomica.simulation.prototypes.HSMD3D: The Box holding the atoms.
box - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
box - Variable in class etomica.simulation.prototypes.LjMd2D
box - Variable in class etomica.simulation.prototypes.LjMd3D
box - Variable in class etomica.simulation.prototypes.SoftSphere3d
box - Variable in class etomica.simulation.prototypes.SwMd2D
box - Variable in class etomica.simulation.prototypes.SWMD3D
box - Variable in class etomica.space.Boundary
box - Variable in class etomica.spin.Heisenberg
box - Variable in class etomica.surfacetension.LJMC
box - Variable in class etomica.surfacetension.SurfaceTensionMapped
box - Variable in class etomica.tests.TestHSMD3D
box - Variable in class etomica.tests.TestLJMC3D
box - Variable in class etomica.tests.TestSWChain
box - Variable in class etomica.thermointegration.LjMc3D
box - Variable in class etomica.threaded.atom.LJMD3DThreaded
box - Variable in class etomica.threaded.domain.LJMD3DThreaded
box - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
box - Variable in class etomica.util.numerical.CalcGradientDifferentiable
box - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
box - Variable in class etomica.virial.MeterVirialBinMultiThreaded
box - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
box - Variable in class etomica.virial.simulations.SimulationVirial
box - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
box - Variable in class etomica.virial.simulations.SimulationVirialOverlap
box - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
box - Variable in class etomica.virial.simulations.SimulationVirialPT
box - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
box - Variable in class etomica.yukawa.TestHC2YukawaMC3D
box - Variable in class etomica.yukawa.TestYukawaMC3D
box - Variable in class etomica.yukawa.TestYukawaMD3D
box - Variable in class etomica.zeolite.ZeoliteSimulation: The Box holding the atoms.
BOX - Static variable in class g3dsys.control.G3DSys
Box - Class in g3dsys.images: Class for drawing a bounding box around the figures in molecule space
Box(G3DSys, short) - Constructor for class g3dsys.images.Box
box1 - Variable in class etomica.dimer.IntegratorDimerRT
box1 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
box1 - Variable in class etomica.simulation.prototypes.GEMCWithRotation
box1 - Variable in class etomica.virial.PotentialCommonAtomic
box2 - Variable in class etomica.dimer.IntegratorDimerRT
box2 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
box2 - Variable in class etomica.simulation.prototypes.GEMCWithRotation
BOX_INDEX - Static variable in class etomica.util.Debug: index of box of interest.
boxA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
boxA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
boxA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
boxA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
BoxAction - Interface in etomica.action: Elementary action performed on a box.
BoxActionAdapter - Class in etomica.action: Convenience class used to define a BoxAction.
BoxActionAdapter() - Constructor for class etomica.action.BoxActionAdapter
boxAdded(IBox) - Method in class etomica.simulation.SimulationEventManager
boxAgentClass - Variable in class etomica.box.BoxAgentManager
BoxAgentManager<E> - Class in etomica.box: BoxAgentManager acts on behalf of client classes (a BoxAgentSource) to manage agents for each Box in a simulation.
BoxAgentManager(BoxAgentManager.BoxAgentSource<E>, Class) - Constructor for class etomica.box.BoxAgentManager
BoxAgentManager(BoxAgentManager.BoxAgentSource<E>, Class, ISimulation) - Constructor for class etomica.box.BoxAgentManager
boxAgentManager - Variable in class etomica.nbr.CriterionSimple
boxAgentManager - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
boxAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
boxAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
boxAgentManager - Variable in class etomica.potential.P1HarmonicSite
BoxAgentManager.AgentIterator<E> - Class in etomica.box: Iterator that loops over the agents, skipping null elements
BoxAgentManager.BoxAgentSource<E> - Interface in etomica.box: Interface for an object that makes an agent to be placed in each atom upon construction.
BoxAgentSiteSource(int, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite.BoxAgentSiteSource
boxAgentSource - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
boxAgentSource - Variable in class etomica.nbr.PotentialMasterNbr
BoxAgentSourceAtomManager<E> - Class in etomica.box
BoxAgentSourceAtomManager(AtomLeafAgentManager.AgentSource<E>, Class) - Constructor for class etomica.box.BoxAgentSourceAtomManager
BoxAgentSourceCellManager - Class in etomica.nbr.cell: BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManager(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.BoxAgentSourceCellManager
BoxAgentSourceCellManagerList - Class in etomica.nbr.list: BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManagerList(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.BoxAgentSourceCellManagerList
BoxAgentSourceCellManagerListMolecular - Class in etomica.nbr.list.molecule: BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
BoxAgentSourceCellManagerListMolecular(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
BoxAgentSourceCellManagerMolecular - Class in etomica.nbr.cell.molecule: BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
BoxAgentSourceCellManagerMolecular(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
BoxAgentSourceCellManagerThreaded - Class in etomica.threaded.domain: BoxAgentSource responsible for creating a NeighborCellManager.
BoxAgentSourceCellManagerThreaded(ISimulation, IAtomPositionDefinition, ISpace) - Constructor for class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
BoxAgentSourceMoleculeManager - Class in etomica.box
BoxAgentSourceMoleculeManager(MoleculeAgentManager.MoleculeAgentSource, ISimulation) - Constructor for class etomica.box.BoxAgentSourceMoleculeManager
boxAtomAdded(IBoxAtomEvent) - Method in interface etomica.api.IBoxListener
boxAtomAdded(IBoxAtomEvent) - Method in class etomica.atom.MoleculeAgentManager
boxAtomAdded(IBoxAtomEvent) - Method in class etomica.box.BoxListenerAdapter
boxAtomAdded(IBoxAtomEvent) - Method in class etomica.integrator.IntegratorMD
BoxAtomEvent - Class in etomica.box: Event that conveys some happening with respect to an Atom in a Box.
BoxAtomEvent(IBox, IAtom) - Constructor for class etomica.box.BoxAtomEvent
BoxAtomIndexEvent - Class in etomica.box: Event that conveys that the maximum global index in a Box has changed.
BoxAtomIndexEvent(IBox, IAtom, int) - Constructor for class etomica.box.BoxAtomIndexEvent
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in interface etomica.api.IBoxListener
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.atom.AtomLeafAgentManager
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.box.BoxListenerAdapter
boxAtomLeafIndexChanged(IBoxAtomIndexEvent) - Method in class etomica.integrator.IntegratorMD
boxAtomRemoved(IBoxAtomEvent) - Method in interface etomica.api.IBoxListener
boxAtomRemoved(IBoxAtomEvent) - Method in class etomica.atom.MoleculeAgentManager
boxAtomRemoved(IBoxAtomEvent) - Method in class etomica.box.BoxListenerAdapter
boxAtomRemoved(IBoxAtomEvent) - Method in class etomica.integrator.IntegratorMD
boxB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
boxB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
boxB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
boxB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
BoxCellManager - Interface in etomica.box: Interface for class that handles assignment of atoms to cells in a box.
boxCells - Variable in class etomica.normalmode.MCMoveAtomSuperBox
BoxCluster - Class in etomica.virial
BoxCluster(ClusterWeight, ISpace) - Constructor for class etomica.virial.BoxCluster: Constructor for BoxCluster.
BoxClusterFactory() - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2.BoxClusterFactory
BoxDeleteMolecules - Class in etomica.action: Deletes molecules from a box as determined by an AtomFilter.
BoxDeleteMolecules(AtomFilter) - Constructor for class etomica.action.BoxDeleteMolecules
boxDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
boxDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
boxDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
boxDim - Variable in class etomica.modules.entropylottery.ModifierDimensions
BoxEvent - Class in etomica.box: Event that conveys some happening with respect to a box or the things it contains.
BoxEvent(IBox) - Constructor for class etomica.box.BoxEvent
BoxEventManager - Class in etomica.box
BoxEventManager(IBox) - Constructor for class etomica.box.BoxEventManager
boxFactory - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in interface etomica.api.IBoxListener
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in class etomica.box.BoxListenerAdapter
boxGlobalAtomIndexChanged(IBoxIndexEvent) - Method in class etomica.integrator.IntegratorMD
BoxGlobalAtomIndexEvent - Class in etomica.box: Event that conveys that the maximum global index in a Box has changed.
BoxGlobalAtomIndexEvent(IBox, int) - Constructor for class etomica.box.BoxGlobalAtomIndexEvent
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in interface etomica.api.IBoxListener
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.atom.AtomLeafAgentManager
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.box.BoxListenerAdapter
boxGlobalAtomLeafIndexChanged(IBoxIndexEvent) - Method in class etomica.integrator.IntegratorMD
boxH - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
boxHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
boxHarmonic - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
boxHarmonic - Variable in class etomica.normalmode.SimOverlap
boxHarmonic - Variable in class etomica.normalmode.SimOverlapLJ
boxHarmonic - Variable in class etomica.normalmode.SimOverlapLJModule
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphere
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
boxHarmonic - Variable in class etomica.normalmode.SimOverlapSSnxy
BoxImposePbc - Class in etomica.action: Action that imposes the central-image effect of a box having periodic boundaries.
BoxImposePbc(ISpace) - Constructor for class etomica.action.BoxImposePbc: Creates the action without specifying a box.
BoxImposePbc(IBox, ISpace) - Constructor for class etomica.action.BoxImposePbc: Creates the action ready to perform on the given box.
BoxImposePbcMolecule(Box, Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
boxIndex - Variable in class etomica.normalmode.P1ConstraintNbr
BoxIndexEvent - Class in etomica.box: Event that conveys that the maximum leaf index in a Box has changed (or is about to change).
BoxIndexEvent(IBox, int) - Constructor for class etomica.box.BoxIndexEvent
BoxInflate - Class in etomica.action: Performs actions that cause volume of system to expand or contract, with molecule positions scaled to keep them in the same relative positions.
BoxInflate(ISpace) - Constructor for class etomica.action.BoxInflate: Constructs action with a default scale of 1.0.
BoxInflate(IBox, ISpace) - Constructor for class etomica.action.BoxInflate: Constructs action ready to be performed on the given box.
boxInflate - Variable in class etomica.liquidLJ.MeterWidomInsertionP
BoxInflateAnisotropic - Class in etomica.action: Class that perform anisotropic angle fluctuation
BoxInflateAnisotropic(ISpace) - Constructor for class etomica.action.BoxInflateAnisotropic
BoxInflateAnisotropic(IBox, ISpace) - Constructor for class etomica.action.BoxInflateAnisotropic
BoxInflateDeformable - Class in etomica.action: Performs actions that cause volume of a deformable system to expand, with molecule positions scaled to keep them in the same relative positions.
BoxInflateDeformable(ISpace) - Constructor for class etomica.action.BoxInflateDeformable
BoxInflateDeformable(IBox, ISpace) - Constructor for class etomica.action.BoxInflateDeformable
BoxInfo - Class in org.jmol.util
BoxInfo() - Constructor for class org.jmol.util.BoxInfo
boxK - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
boxL - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
boxLiquid - Variable in class etomica.modules.vle.VLESim
BoxListenerAdapter - Class in etomica.box
BoxListenerAdapter() - Constructor for class etomica.box.BoxListenerAdapter
boxManager - Variable in class etomica.normalmode.P1ConstraintNbr
boxMin - Variable in class etomica.dimer.IntegratorDimerMin
boxMoleculeAdded(IBoxMoleculeEvent) - Method in interface etomica.api.IBoxListener
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.atom.AtomLeafAgentManager
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.atom.MoleculeAgentManager
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.box.BoxListenerAdapter
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.integrator.IntegratorHard
boxMoleculeAdded(IBoxMoleculeEvent) - Method in class etomica.integrator.IntegratorMD
BoxMoleculeAddedEvent - Class in etomica.box: Event that conveys that an Atom has been added to a Box.
BoxMoleculeAddedEvent(IBox, IMolecule) - Constructor for class etomica.box.BoxMoleculeAddedEvent
BoxMoleculeCountEvent - Class in etomica.box
BoxMoleculeCountEvent(IBox, ISpecies, int) - Constructor for class etomica.box.BoxMoleculeCountEvent
BoxMoleculeEvent - Class in etomica.box
BoxMoleculeEvent(IBox, IMolecule) - Constructor for class etomica.box.BoxMoleculeEvent
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in interface etomica.api.IBoxListener
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in class etomica.box.BoxListenerAdapter
boxMoleculeIndexChanged(IBoxMoleculeIndexEvent) - Method in class etomica.integrator.IntegratorMD
BoxMoleculeIndexEvent - Class in etomica.box: Event that conveys that an Atom's global index in a box has changed.
BoxMoleculeIndexEvent(IBox, IMolecule, int) - Constructor for class etomica.box.BoxMoleculeIndexEvent
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in interface etomica.api.IBoxListener
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.atom.AtomLeafAgentManager
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.atom.MoleculeAgentManager
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.box.BoxListenerAdapter
boxMoleculeRemoved(IBoxMoleculeEvent) - Method in class etomica.integrator.IntegratorMD
BoxMoleculeRemovedEvent - Class in etomica.box: Event that conveys that an Atom has been removed from a Box.
BoxMoleculeRemovedEvent(IBox, IMolecule) - Constructor for class etomica.box.BoxMoleculeRemovedEvent
boxNeighborsUpdated(IBoxEvent) - Method in class etomica.box.BoxListenerAdapter
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in interface etomica.api.IBoxListener
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in class etomica.atom.MoleculeAgentManager
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in class etomica.box.BoxListenerAdapter
boxNumberMolecules(IBoxMoleculeCountEvent) - Method in class etomica.integrator.IntegratorMD
boxPanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
BoxQuench - Class in etomica.action: Scales all velocities of a box so that its kinetic temperature is equal to a given value.
BoxQuench(int) - Constructor for class etomica.action.BoxQuench
BoxQuench(double, int) - Constructor for class etomica.action.BoxQuench: Constructs class without specifying box and using Default temperature.
BoxQuench(IBox, double) - Constructor for class etomica.action.BoxQuench: Constructs class ready to perform quench on given box to given temperature.
BoxRandomizeMomenta - Class in etomica.action: Randomizes the velocities of all the leaf atoms in an IBox based on the Maxwell-Boltzmann distribution.
BoxRandomizeMomenta(IBox, IRandom) - Constructor for class etomica.action.BoxRandomizeMomenta
boxRef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage
boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
boxRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
boxRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
boxRef - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
boxRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
boxRemoved(IBox) - Method in class etomica.simulation.SimulationEventManager
boxScale - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
BoxScaleMomenta - Class in etomica.action: Scales the momenta of all the leaf atoms in an IBox such that the kinetic temperature matches some value.
BoxScaleMomenta(IBox, ISpace) - Constructor for class etomica.action.BoxScaleMomenta
boxSize - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
boxSize - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
boxSize - Variable in class etomica.potential.EwaldSummation
boxSize - Variable in class etomica.potential.EwaldSumMolecules
boxSize0 - Variable in class etomica.normalmode.MeterDisplacementRMS
boxTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
boxTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
boxTarg - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
boxTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
boxTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage
boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
boxTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
boxTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
boxTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
boxTarget - Variable in class etomica.normalmode.SimOverlap
boxTarget - Variable in class etomica.normalmode.SimOverlapLJ
boxTarget - Variable in class etomica.normalmode.SimOverlapLJModule
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
boxTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
BoxTracker() - Constructor for class etomica.integrator.IntegratorPT.BoxTracker
boxVapor - Variable in class etomica.modules.vle.VLESim
boxVec - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
boxWellManager - Variable in class etomica.potential.P2SquareWellRobust
bpharm - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
bpharm - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
bpharmLJ - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
bpharmLJ - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
bpRes - Variable in class etomica.normalmode.MeterSolidDACut
bpResDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
bprime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
branch - Static variable in class org.jmol.script.Token
BravaisLattice - Class in etomica.lattice: Arbitrary-dimension Bravais Lattice, in which the sites are instances of etomica.space.Vector, with positions given as linear combinations of a set of primitive vectors.
BravaisLattice(Primitive) - Constructor for class etomica.lattice.BravaisLattice
BravaisLatticeCrystal - Class in etomica.lattice: A lattice with sites given by the "atom" sites of a crystal.
BravaisLatticeCrystal(Primitive, Basis) - Constructor for class etomica.lattice.BravaisLatticeCrystal: Constructs a lattice having sites given by the "atom" sites of the given crystal.
BreadthFirst - Class in etomica.graph.traversal
BreadthFirst() - Constructor for class etomica.graph.traversal.BreadthFirst
brillouin - Static variable in class org.jmol.script.Token
broadhurstBBP(int, int, int[], MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Broadhurst ladder sequence.
broken - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
broken3body - Static variable in class etomica.models.water.P2WaterSzalewicz
bScaled - Variable in class org.jmol.util.Rgb16
bsDisplay - Variable in class org.jmol.util.MeshSurface
bsNull - Static variable in class org.jmol.util.BitSetUtil
bsPolygons - Variable in class org.jmol.util.MeshSurface
bsSelectRange(Token, int) - Static method in class org.jmol.script.ScriptVariable
bsSelectToken(Token) - Static method in class org.jmol.script.ScriptVariable
bsSelectVar(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
bsSlabGhost - Variable in class org.jmol.util.MeshSurface
bSum - Variable in class etomica.virial.ClusterSinglyConnected
buf - Variable in class etomica.util.RandomNumberGeneratorUnix
bufferSize - Variable in class org.jmol.util.GData
BuilderCollectionPotential - Class in etomica.virial.GUI.components
BuilderCollectionPotential() - Constructor for class etomica.virial.GUI.components.BuilderCollectionPotential
bump(IAtomList, double) - Method in class etomica.modules.adsorption.P1Wall
bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBonding: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellSurface: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
bump(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
bump(IAtomList, double) - Method in class etomica.modules.colloid.P1Wall
bump(IAtomList, double) - Method in class etomica.modules.mu.P1MagicWall
bump(IAtomList, double) - Method in class etomica.modules.mu.P2SquareWellOneSide: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.modules.osmosis.P1HardWall
bump(IAtomList, double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
bump(IAtomList, double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
bump(IAtomList, double) - Method in class etomica.normalmode.P2XOrder
bump(IAtomList, double) - Method in class etomica.potential.P1HardBoundary
bump(IAtomList, double) - Method in class etomica.potential.P1HardMovingBoundary
bump(IAtomList, double) - Method in class etomica.potential.P1HardPeriodic: Performs no action.
bump(IAtomList, double) - Method in class etomica.potential.P2DoubleWell: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2HardAssociation: Implements the collision dynamics.
bump(IAtomList, double) - Method in class etomica.potential.P2HardBond: Implements collision dynamics for pair attempting to separate beyond tether distance
bump(IAtomList, double) - Method in class etomica.potential.P2HardBondedList
bump(IAtomList, double) - Method in class etomica.potential.P2HardSphere: Implements collision dynamics and updates lastCollisionVirial
bump(IAtomList, double) - Method in class etomica.potential.P2HardWrapper
bump(IAtomList, double) - Method in class etomica.potential.P2Ideal: Does nothing.
bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableBond: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableSphere: Implements collision dynamics between two penetrable-sphere atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableSquareWell: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2RoughSphere: Implements collision dynamics and updates lastCollisionVirial Assumes atoms have same size and mass
bump(IAtomList, double) - Method in class etomica.potential.P2SquareWell: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2SquareWellRobust: Implements collision dynamics between two square-well atoms.
bump(IAtomList, double) - Method in class etomica.potential.P2Tether: Implements collision dynamics for pair attempting to separate beyond tether distance
bump(IAtomList, double) - Method in interface etomica.potential.PotentialHard: Implements the collision dynamics.
button - Variable in class etomica.graphics.DeviceButton
button - Variable in class etomica.zeolite.DeviceButtonSingle
buttonActions - Variable in class etomica.graphics.DeviceButtonGroup
buttonCorner1 - Variable in class etomica.util.Grabber
buttonCorner2 - Variable in class etomica.util.Grabber
buttonGroup - Variable in class etomica.graphics.DeviceButtonGroup
buttonPanel - Variable in class etomica.graphics.DeviceButtonGroup
buttons - Variable in class etomica.graphics.DeviceButtonGroup
bv - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
bv - Variable in class etomica.models.OPLS.P2AceticAcidTwoSite
bv - Variable in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
bveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
bveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
bvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
bvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
bveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
bveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
bVirial - Variable in class etomica.util.numerical.B9Optimizer
bVirial - Variable in class etomica.util.numerical.VirialOptimizer
bVirialFromFile - Variable in class etomica.util.numerical.B9Optimizer
bVirialFromFile - Variable in class etomica.util.numerical.VirialOptimizer
bvso - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
bvso - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites

C

c - Variable in class etomica.dimer.P1LepsHarmonic
c - Variable in class etomica.liquidLJ.LjMd3D.VolumeBias
c - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
C - Static variable in class etomica.math.Gamma
C - Variable in class etomica.meam.PotentialFeEAM
c - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
C - Variable in class etomica.models.nitrogen.P2Nitrogen
C - Variable in class etomica.models.nitrogen.P2NitrogenAB
C - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
c - Static variable in class etomica.models.water.P2WaterSzalewicz
c - Variable in class etomica.normalmode.SoftSphereSolidEOS
c - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
c - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
C - Variable in class etomica.potential.P2HePCKLJS
c - Static variable in class etomica.potential.P2WaterPotentialsJankowski
c - Static variable in class etomica.statmech.HardSphereSolid
c - Variable in class etomica.util.numerical.PadeApproximation
c - Variable in class etomica.util.numerical.PadeApproximation.VirialParam
c - Variable in class etomica.virial.ClusterPY
c0 - Variable in class etomica.graphics.DisplayTable
c0 - Variable in class etomica.meam.PotentialCuLREP
c0 - Variable in class etomica.meam.PotentialEFS
c1 - Variable in class etomica.mappedvirial.MappedUpotential
c1 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
c1 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
c1 - Variable in class etomica.meam.PotentialCuLREP
c1 - Variable in class etomica.meam.PotentialEFS
c1 - Variable in class etomica.modules.adsorption.EOSSWPatel
c10 - Static variable in class etomica.potential.P1HydrogenMielke
C10Data - Variable in class etomica.potential.P2QChemInterpolated
C1CH31 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C1CH31 - Variable in class etomica.association.BiasVolumeAceticAcid
C1DBO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C1DBO1 - Variable in class etomica.association.BiasVolumeAceticAcid
C1SBO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C1SBO1 - Variable in class etomica.association.BiasVolumeAceticAcid
c2 - Variable in class etomica.meam.PotentialCuLREP
c2 - Variable in class etomica.meam.PotentialEFS
c2 - Variable in class etomica.modules.adsorption.EOSSWPatel
c2 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c2_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
C2C1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C2C1 - Variable in class etomica.association.BiasVolumeAceticAcid
C2CH32 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C2CH32 - Variable in class etomica.association.BiasVolumeAceticAcid
C2DBO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C2DBO2 - Variable in class etomica.association.BiasVolumeAceticAcid
C2SBO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
C2SBO2 - Variable in class etomica.association.BiasVolumeAceticAcid
c3 - Variable in class etomica.meam.PotentialCuLREP
c3 - Variable in class etomica.meam.PotentialEFS
c3 - Static variable in class etomica.models.water.P2WaterSzalewicz
c3 - Variable in class etomica.modules.adsorption.EOSSWPatel
c3 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
C3 - Static variable in class etomica.virial.cluster.Standard
c3_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c3Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c3Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c4 - Variable in class etomica.meam.PotentialCuLREP
c4 - Variable in class etomica.meam.PotentialEFS
c4 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c4_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c4Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c4Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c5 - Variable in class etomica.potential.P2HydrogenHinde
c5 - Variable in class etomica.potential.P2HydrogenHindeAtomic
c5 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c5_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c5Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c5Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
C6 - Variable in class etomica.models.co2.P2CO2Hellmann
c6 - Static variable in class etomica.potential.P1HydrogenMielke
c6 - Variable in class etomica.potential.P2HydrogenHinde
c6 - Variable in class etomica.potential.P2HydrogenHindeAtomic
c6 - Variable in class etomica.potential.P2NitrogenHellmann
c6 - Static variable in class etomica.potential.P2O2Bartolomei
c6 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c6_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
C6A - Static variable in class etomica.models.co2.P2CO2Hellmann
c6A - Static variable in class etomica.potential.P2NitrogenHellmann
c6Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c6Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
C6B - Static variable in class etomica.models.co2.P2CO2Hellmann
c6B - Static variable in class etomica.potential.P2NitrogenHellmann
C6BO - Static variable in class etomica.potential.P2HePCKLJS
C6Data - Variable in class etomica.potential.P2QChemInterpolated
c7Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
c7Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
C8 - Variable in class etomica.models.co2.P2CO2Hellmann
c8 - Static variable in class etomica.potential.P1HydrogenMielke
c8 - Variable in class etomica.potential.P2HydrogenHinde
c8 - Variable in class etomica.potential.P2HydrogenHindeAtomic
c8 - Static variable in class etomica.potential.P2O2Bartolomei
C8A - Static variable in class etomica.models.co2.P2CO2Hellmann
C8B - Static variable in class etomica.models.co2.P2CO2Hellmann
C8Data - Variable in class etomica.potential.P2QChemInterpolated
C9iso - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
C9isoSim - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
cA - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
cA2nD - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
cAB - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
calc(double[][]) - Method in class org.jmol.util.Eigen: Check for symmetry, then construct the eigenvalue decomposition
CalcAnalytical2ndDerivativeNitrogen - Class in etomica.models.nitrogen: Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcAnalytical2ndDerivativeNitrogen(ISpace, IBox, P2Nitrogen, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
CalcAnalytical2ndDerivativeNitrogen(ISpace, IBox, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double) - Constructor for class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
calcAngle(IVector, IVector) - Method in class etomica.association.BiasVolume2SiteAceticAcid
calcAngle(IVector, IVector) - Method in class etomica.association.BiasVolumeAceticAcid
calcApprox - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
calcApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
calcApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
calcApprox - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
calcApprox - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
calcApprox - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
calcApprox - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
calcApprox - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
calcAveCosThetaInitial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
calcAveragePoint(Point3f, Point3f, Point3f) - Static method in class org.jmol.util.Measure
calcAveragePointN(Point3f[], int, Point3f) - Static method in class org.jmol.util.Measure
calcB2(double, double) - Static method in class etomica.modules.vle.VirialLJQB2
calcBestAxisThroughPoints(Point3f[], Point3f, Vector3f, Vector3f, int) - Static method in class org.jmol.util.Measure
calcBMu(double, double, double) - Static method in class etomica.metastable.LJmuVT
calcBondAngleEnergy(double) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcBondAngleEnergy(double) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
calcBondL() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcBondL() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane: Returns the bond length for the new atom in a test Should take bonded potential into account.
calcBondTorsionalEnergy(IVectorMutable) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcBondTorsionalEnergy(IVectorMutable) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
calcBoth(double, double) - Method in class etomica.math.Gamma
calcConversion(IMoleculeList) - Method in class etomica.modules.chainequilibrium.MeterConversion
calcdMudP(double, double) - Static method in class etomica.statmech.HardSphereSolid
calcdmudrho(double, double) - Static method in class etomica.statmech.HardSphereSolid
calcdPdrho(double, double) - Static method in class etomica.statmech.HardSphereSolid
calcer - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MyTypeAgent
calcErr(int, int) - Method in class etomica.util.numerical.AkimaSplineSmoother
calcErr(int, int) - Method in class etomica.util.numerical.AkimaSplineSmootherDy
calcExternalEnergy(IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcExternalEnergy(IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
calcF(double) - Method in class etomica.virial.MayerFunctionThreeBody: Returns exp(x)-1 computed directly or using a series expansion
calcfAB(int, boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
calcfAB0(boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
calcFacs() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
calcfC(boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
CalcFFT - Class in etomica.virial: CalcFFT can calculate distribution functions using FFT.
CalcFFT(IFunction, double, int) - Constructor for class etomica.virial.CalcFFT
calcForce(int, double) - Method in class etomica.threads.ThreadsMD
calcfQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening: This calculates all fQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterSumHS: This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW: This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS: This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibody
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyMix
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft: This calculates all FQ values given that the entries for pairs have already been populated.
calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD: This calculates all FQ values given that the entries for pairs have already been populated.
calcGageLength() - Method in class etomica.modules.materialfracture.MeterElongation
calcGageLength() - Method in class etomica.modules.materialfracture.MeterStrain
calcGamma(double, double) - Method in class etomica.math.Gamma: Return the normalized complementary incomplete gamma function, (integral from t=x to t=inf of exp(-t)*t^(a-1)) / gamma(a) if a>0 or (integral from t=x to t=inf of exp(-t)*t^(a-1)) * exp(x)*x^(-a) if a<=0
calcGammaStar(double, double) - Method in class etomica.math.Gamma: Return the normalized incomplete gamma function, (integral from t=0 to t=x of exp(-t)*t^(a-1)) / x^a if a>0 If a=0 and x=0, gammaStar is indeterminate and an exception is thrown.
calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerLJadatom
calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerMEAMadatom
calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerMEAMGB
calcGradientDifferentiable - Variable in class etomica.kmc.SimKMCMEAMadatom
CalcGradientDifferentiable - Class in etomica.util.numerical: Uses finite difference methods to determine the second order differential of the potential (i.e.
CalcGradientDifferentiable(IBox, IPotentialMaster, IMoleculeList, ISpace) - Constructor for class etomica.util.numerical.CalcGradientDifferentiable
calcGreyscaleRgbFromRgb(int) - Static method in class org.jmol.util.ColorUtil: Return a greyscale rgb value 0-FF using NTSC color luminance algorithm
CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen - Class in etomica.models.nitrogen: Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen(ISpace, IBox, P2Nitrogen, CoordinateDefinitionNitrogen, boolean) - Constructor for class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen(ISpace, IBox, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double, boolean) - Constructor for class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
CalcHarmonicA - Class in etomica.normalmode: Convenience class to calculate the Helmholtz free energy based on the normal mode description of the system with harmonic springs governing the system's exploration of the modes.
CalcHarmonicA() - Constructor for class etomica.normalmode.CalcHarmonicA
CalcJacobian - Class in etomica.normalmode: Class that calculates the dq/dx Jacobian.
CalcJacobian() - Constructor for class etomica.normalmode.CalcJacobian
calcLegendrePolynomial(int, double) - Static method in class etomica.math.SpecialFunctions: Calculates Pn(x), Legendre polynomial of order n for the given input value.
calcModes - Variable in class etomica.dimer.SimDimerLJadatom
calcMu - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
CalcNumerical2ndDerivative - Class in etomica.models.nitrogen: Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcNumerical2ndDerivative(IBox, PotentialMaster, CoordinateDefinition) - Constructor for class etomica.models.nitrogen.CalcNumerical2ndDerivative
CalcNumerical2ndDerivativeNitrogen - Class in etomica.models.nitrogen: Determine the second derivative of the atomic/ molecular potential energy w.r.t.
CalcNumerical2ndDerivativeNitrogen(IBox, P2Nitrogen, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
CalcNumerical2ndDerivativeNitrogen(IBox, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double) - Constructor for class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
calcOrientation(IMolecule, IOrientationFull3D) - Method in interface etomica.atom.OrientationCalc: Calculates the orientation of the given molecule and stores that in the given orientation.
calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.atom.OrientationCalcAtom
calcOrientation(IMolecule, double[]) - Method in interface etomica.atom.OrientationCalcQuaternion
calcOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater3P
calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater3P
calcOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater4P
calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater4P
calcpPade(int, int, double) - Method in class etomica.util.numerical.VirialOptimizer
calcpVirial(double) - Method in class etomica.util.numerical.B9Optimizer
calcRandomBond() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane: Generates a random bond.
calcRandomBondWithAngle(IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcRandomBondWithAngle(IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane: XXX METHOD NOT TESTED! USE AT OWN PERIL! Generates a random bond that accounts for bond angle in the calculation This method will change its parameter.
calcRandomBondWithAngleAndTorsion(IAtom, IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcRandomBondWithAngleAndTorsion(IAtom, IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane: XXX METHOD NOT TESTED! USE AT OWN PERIL!l dy Generates a random bond that accounts for bond angle and torsion in the calculation.
calcRates() - Method in class etomica.kmc.IntegratorKMC
calcRates() - Method in class etomica.kmc.IntegratorKMCCluster
calcReeHoover() - Method in class etomica.virial.cluster.ClusterGenerator: Calculates the Ree-Hoover coefficient (coefficient for Ree-Hoover diagram / coefficient for Mayer diagram) for mCluster and sets mCluster's mReeHooverFactor to it.
calcReeHooverCoefficient(Graph, int, byte) - Method in class etomica.graph.operations.ReeHoover
calcRosenbluthFactors() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane: Calculates wOld and wNew
calcRosenbluthFactors() - Method in class etomica.models.hexane.MCMoveCBMC
calcRotationRadius(Point3f) - Method in class g3dsys.control.G3DSys: Finds the atom distance furthest from the given point; for rotation
calcScore(int[]) - Method in class etomica.virial.cluster.ClusterDiagram: compute a score for the cluster.
calcSignature(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
calcSignatures() - Method in class etomica.virial.ClusterWheatleyPartitionScreening: Compute signatures used for lookup tables of fA, fAB, fC
calcSphereShading() - Static method in class org.jmol.util.Shader
calcStartIndex() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
calcStartIndex() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
calcSums(IAtomList) - Method in class etomica.meam.PotentialMEAM
calcSupport(AtomTypeSpheroPolyhedron, IVectorMutable) - Method in class etomica.potential.P2SpheroPolyhedron
calcT(IVector, double[], double[]) - Method in class etomica.normalmode.CoordinateDefinition: Calculates the complex "T vector", which is collective coordinate given by the Fourier sum (over atoms) of the generalized coordinate vector.
calcU(IMoleculeList) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
calcU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
calcU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
calcU(IVectorMutable) - Method in class etomica.models.nitrogen.TestRotationVector
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinition: Calculates the generalized coordinates for the given molecules in their current position and orientation.
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionLeaf: Assigns the given array u to be the current position of the atom minus its lattice position
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
calcU(IMoleculeList) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in interface etomica.api.IPotentialMaster: Performs the given PotentialCalculation on the atoms of the given Box.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.dimer.PotentialMasterListDimer
calculate() - Method in class etomica.models.oneDHardRods.DoubleIntegralEtas
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.list.PotentialMasterList: Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList: Performs given PotentialCalculation using potentials/neighbors associated with the given atom (if any).
calculate(IAtom, IteratorDirective.Direction, PotentialCalculation, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.PotentialMasterHybrid: Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.site.PotentialMasterSite: Overrides superclass method to enable direct neighbor-list iteration instead of iteration via species/potential hierarchy.
calculate(IAtom, PotentialCalculation) - Method in class etomica.nbr.site.PotentialMasterSite: Performs given PotentialCalculation using potentials/neighbors associated with the given atom (if any).
calculate(MoleculesetIterator, IteratorDirective.Direction, IAtom, PotentialCalculation) - Method in class etomica.potential.PotentialGroup: Performs the specified calculation over the iterates given by the iterator, using the directive to set up the iterators for the sub-potentials of this group.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMaster
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMasterLrc: Performs given PotentialCalculation on all LRC potentials added to this group.
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMasterMonatomic
calculate(IAtom, IAtomList, int, PotentialArrayByType, IteratorDirective.Direction, PotentialCalculation) - Method in class etomica.potential.PotentialMasterMonatomic
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
calculate(IAtom, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.atom.PotentialMasterListWorker
calculate(IBox, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
calculate(IAtom, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.domain.PotentialMasterListWorker
calculateEnergy(IBox) - Method in interface etomica.normalmode.IAPIPotential: Returns the potential energy of the given box.
calculateEnergy(IBox) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
calculateEnergy(IBox) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
calculateEnergy(double) - Method in class etomica.potential.P22CLJQ
calculateForces() - Method in class etomica.integrator.IntegratorGear4
calculateForces() - Method in class etomica.integrator.IntegratorGear4NPH
calculateLatticeDimensions(int, IVector) - Method in class etomica.config.ConfigurationLattice
calculateLatticeDimensions(int, IVector) - Method in class etomica.config.ConfigurationLatticeSimple
calculateLatticeDimensions(int, IVectorMutable) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
calculateLatticeDimensions(int, IVectorMutable) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
calculateLatticeDimensions(int, IVector) - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
calculateModes() - Method in class etomica.normalmode.NormalModesMolecular
calculateModes() - Method in class etomica.normalmode.NormalModesPotential
calculateModes() - Method in class etomica.normalmode.NormalModesSoftSpherical
calculateModes() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
calculateQuaternionRotation(Point3f[][], float[]) - Static method in class org.jmol.util.Measure
calculateRangeIndependent(IMolecule, IteratorDirective.Direction, IAtom, PotentialCalculation) - Method in class etomica.nbr.PotentialGroupNbr: Performs the specified calculation over the iterates given by the iterator, using the directive to set up the iterators for the sub-potentials of this group.
calculateSum(FunctionGeneral) - Method in class etomica.lattice.LatticeSum
calculateSum(FunctionGeneral) - Method in class etomica.lattice.LatticeSumCrystal
calculateSum(FunctionGeneral) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
calculateSum(LatticeSumMolecularCrystal.AtomicTensorAtomicPair) - Method in class etomica.normalmode.LatticeSumMolecularCrystal
calculateSum(LatticeEnergyParacetamol) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
calculateSystemSigmaHSRef(ModelSelectedSpecies) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
calculateSystemSigmaHSRef(IMolecularModel_SpeciesFactory[], int[]) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
calculateThreaded(IBox, IteratorDirective, IPotentialCalculationThreaded, NeighborListManager) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
calculateThreaded(IBox, IteratorDirective, IPotentialCalculationThreaded, NeighborListManager) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
calcValue() - Method in class etomica.virial.ClusterChainHS
calcValue() - Method in class etomica.virial.ClusterChainSoft
calcValue(BoxCluster) - Method in class etomica.virial.ClusterICPYC
calcValue(BoxCluster) - Method in class etomica.virial.ClusterPY
calcValue() - Method in class etomica.virial.ClusterSinglyConnected
calcValue() - Method in class etomica.virial.ClusterSum
calcValue() - Method in class etomica.virial.ClusterSumAssociation
calcValue() - Method in class etomica.virial.ClusterSumExternalField
calcValue(BoxCluster) - Method in class etomica.virial.ClusterSumHS: Returns the cluster value for the given configuration.
calcValue() - Method in class etomica.virial.ClusterSumIC
calcValue() - Method in class etomica.virial.ClusterSumMultibody
calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
calcValue() - Method in class etomica.virial.ClusterSumStickyEF
calcValue(BoxCluster) - Method in interface etomica.virial.ClusterWheatley: Calculates the value of the configuration.
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW: Returns the cluster value for the given configuration.
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS: Returns the cluster value for the given configuration.
calcValue(BoxCluster, boolean) - Method in class etomica.virial.ClusterWheatleyHS
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibody
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyMix
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening: Returns the cluster value for the given configuration.
calcValue(BoxCluster, boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft: Returns the cluster value for the given configuration.
calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD: Returns the cluster value for the given configuration.
CalcVibrationalModes - Class in etomica.action: Calculates the eigenvalues of an NxN matrix.
CalcVibrationalModes() - Constructor for class etomica.action.CalcVibrationalModes
calcVibrationalModes - Variable in class etomica.dimer.SimDimerLJadatom
calcVibrationalModes - Variable in class etomica.dimer.SimDimerMEAMadatom
calcVibrationalModes - Variable in class etomica.dimer.SimDimerMEAMGB
calcVibrationalModes - Variable in class etomica.kmc.SimKMCMEAMadatom
calcWeight() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
calcXs(double, double) - Method in class etomica.mappedvirial.MappedUpotential
calcXs(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
calcXs(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
calcZbufferLimits() - Method in class g3dsys.control.G3DSys
callCount - Variable in class etomica.data.meter.MeterRDF
callCount - Variable in class etomica.data.meter.MeterRDFPC
callCount - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
called - Static variable in class etomica.graph.isomorphism.Match
Calorie - Class in etomica.units: The Joule unit of energy, equal to 1 N-m or 1 kg-m^2/s^2.
cameradepth - Static variable in class org.jmol.script.Token
cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
cAN2nD - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
cancelMap - Variable in class etomica.virial.cluster.VirialDiagrams
cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsMix
cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsMix2
cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsPT
cancelMap - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
cancelMap - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
cancelP - Variable in class etomica.virial.cluster.VirialDiagramsMix
cancelP - Variable in class etomica.virial.cluster.VirialDiagramsMix2
cancelP - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
cancelP - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
Candela - Class in etomica.units: The candela is the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian.
canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
canIncrement() - Method in class org.jmol.script.ScriptVariable
canMoveLeft() - Method in class etomica.graph.engine.ConsoleUI
canMoveRight() - Method in class etomica.graph.engine.ConsoleUI
canvas - Variable in class etomica.graphics.DisplayBox
canvas - Variable in class etomica.graphics.DisplayPolytope
cap - Static variable in class org.jmol.script.Token
capAABond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capABBond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capBABond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capBBBond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
capF1Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capF2Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capFABBond - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
capFABBond - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
capFABBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
capFACBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFACBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capFBABond - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
capFBABond - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
capFBABond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
capFBCBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFBCBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capFBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
capFBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capFCABond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFCABond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capFCBBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
capFCBBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
capitalize(String) - Static method in class etomica.util.Strings: Capitalizes the first letter of the given string.
carbohydrate - Static variable in class org.jmol.script.Token
Carbon - Class in etomica.chem.elements: Class for the Carbon element.
Carbon(String) - Constructor for class etomica.chem.elements.Carbon
Carbon(String, double) - Constructor for class etomica.chem.elements.Carbon
cardinality() - Method in class org.jmol.util.BitSet: Returns the number of bits set to true in this BitSet.
cardinalityN(int) - Method in class org.jmol.util.BitSet
cardinalityOf(BitSet) - Static method in class org.jmol.util.BitSetUtil: cardinality = "total number of set bits"
cartA - Static variable in class etomica.potential.P2WaterPotentialsJankowski
cartB - Static variable in class etomica.potential.P2WaterPotentialsJankowski
CartesianIterator - Class in etomica.graph.iterators
CartesianIterator() - Constructor for class etomica.graph.iterators.CartesianIterator
CartesianPermutator - Class in etomica.graph.iterators
CartesianPermutator(int[], int[]) - Constructor for class etomica.graph.iterators.CartesianPermutator
cartoon - Static variable in class org.jmol.script.Token
cartoonbaseedges - Static variable in class org.jmol.script.Token
cartoonfancy - Static variable in class org.jmol.script.Token
cartoonrockets - Static variable in class org.jmol.script.Token
CastGroupOfTablesToDataTable - Class in etomica.data.types: A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
CastGroupOfTablesToDataTable() - Constructor for class etomica.data.types.CastGroupOfTablesToDataTable: Sole constructor.
CastGroupToDoubleArray - Class in etomica.data.types: A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
CastGroupToDoubleArray() - Constructor for class etomica.data.types.CastGroupToDoubleArray: Sole constructor.
CastToDouble - Class in etomica.data.types: A DataProcessor that converts a Data instance into a DataDouble.
CastToDouble() - Constructor for class etomica.data.types.CastToDouble: Sole constructor.
CastToDoubleArray - Class in etomica.data.types: A DataProcessor that converts a Data instance into a DataDoubleArray.
CastToDoubleArray() - Constructor for class etomica.data.types.CastToDoubleArray: Sole constructor.
CastToGroup - Class in etomica.data.types: A DataProcessor that effectively wraps a Data instance into a DataGroup.
CastToGroup() - Constructor for class etomica.data.types.CastToGroup: Sole constructor.
CastToTable - Class in etomica.data.types: A DataProcessor that converts a Data instance into a DataTable.
CastToTable() - Constructor for class etomica.data.types.CastToTable: Sole constructor.
Catalysis - Class in etomica.modules.catalysis: Simulation for Catalysis module.
Catalysis(ISpace, int) - Constructor for class etomica.modules.catalysis.Catalysis
CatalysisAgent() - Constructor for class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
CatalysisGraphic - Class in etomica.modules.catalysis: Catalysis graphical app.
CatalysisGraphic(Catalysis, ISpace, boolean) - Constructor for class etomica.modules.catalysis.CatalysisGraphic
CatalysisGraphic.Applet - Class in etomica.modules.catalysis
cavityDipole - Variable in class etomica.potential.P2ReactionFieldDipole
cavityDipole - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
cB - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
CBMCGrowSolidHexane - Class in etomica.models.hexane: Contains specifics for the solid hexane model: bond length = 0.4 rejects moving the whole molecule as a CBMC move
CBMCGrowSolidHexane(IPotentialMaster, IRandom, ISpace, IntegratorMC, IBox, ISpecies, int) - Constructor for class etomica.models.hexane.CBMCGrowSolidHexane
CBMCGrowStraightAlkane - Class in etomica.models.hexane: Grows a straight-chain alkane of specified length.
CBMCGrowStraightAlkane(IPotentialMaster, IRandom, IntegratorMC, IBox, ISpecies, ISpace, int, int) - Constructor for class etomica.models.hexane.CBMCGrowStraightAlkane
cbmcMove - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
cbrt(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The cube root.
cc - Static variable in class etomica.statmech.HardSphereSolid
CCbondL - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
CCbondL - Variable in class etomica.virial.ConformationAlkaneEH
cclec - Static variable in class etomica.potential.P2O2Bartolomei
ccpol2Angles - Static variable in class etomica.potential.P2WaterPotentialsJankowski
ccpol2BL - Static variable in class etomica.potential.P2WaterPotentialsJankowski
cctMove - Variable in class etomica.models.hexane.TestHexane
cctMove - Variable in class etomica.models.hexane.TestHexaneFileConfig
cctMove - Variable in class etomica.models.hexane.TestSetToUHexane
cdataIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
cDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
cDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
cDefR - Variable in class etomica.models.oneDHardRods.DoubleIntegralEtas
cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage
cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
cDefT - Variable in class etomica.models.oneDHardRods.DoubleIntegralEtas
cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage
cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
cDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
cDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
cDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
cDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
cDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
cdum - Variable in class etomica.potential.P2HydrogenPatkowski
cdum - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
cdz - Static variable in class etomica.statmech.HardSphereSolid
ceil() - Method in class etomica.veos.bigdecimal.Rational: ceil(): the nearest integer not smaller than this.
Cell - Class in etomica.nbr.cell: Site used to form array of cells for cell-based neighbor listing.
Cell(int) - Constructor for class etomica.nbr.cell.Cell
cell - Static variable in class org.jmol.script.Token
Cell.CellFactory - Class in etomica.nbr.cell
CellFactory() - Constructor for class etomica.nbr.cell.Cell.CellFactory
CellFactory() - Constructor for class etomica.nbr.cell.molecule.CellMolecular.CellFactory
CellLattice - Class in etomica.lattice: A lattice of arbitrarily-sized rectangular cells, such that a point in space can be associated with one of the cells.
CellLattice(ISpace, IVector, SiteFactory) - Constructor for class etomica.lattice.CellLattice
CellLattice.NeighborIterator - Class in etomica.lattice: Extends the SimpleLattice neighbor iterator to provide methods that specify the neighbor range in terms of a distance, rather than an index range.
CellMolecular - Class in etomica.nbr.cell.molecule: Site used to form array of cells for cell-based neighbor listing.
CellMolecular(int) - Constructor for class etomica.nbr.cell.molecule.CellMolecular
CellMolecular.CellFactory - Class in etomica.nbr.cell.molecule
cellPosition - Variable in class etomica.normalmode.CoordinateDefinition.BasisCell
cellRange - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
cellRange - Variable in class etomica.nbr.cell.NeighborCellManager
cells - Variable in class etomica.normalmode.CoordinateDefinition
cells - Variable in class etomica.normalmode.MCMoveAtomSuperBox
cellSizeX - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
cellSizeX - Variable in class etomica.modules.sam.ConfigurationSAM
cellSizeZ - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
cellSizeZ - Variable in class etomica.modules.sam.ConfigurationSAM
center - Variable in class etomica.atom.AtomPositionGeometricCenterPBC
CENTER - Static variable in class etomica.graphics.DisplayBox
CENTER - Static variable in class etomica.graphics.DisplayPolytope
center - Variable in class etomica.modules.crystalviewer.CrystalViewer
center - Variable in class etomica.modules.droplet.ConfigurationDroplet
center - Variable in class etomica.modules.droplet.MeterDeformation
center - Variable in class etomica.modules.rheology.IntegratorPolymer
center - Static variable in class org.jmol.script.Token
center - Static variable in class org.jmol.viewer.JmolConstants
centerAtomColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
centerer - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
centerMass - Variable in class etomica.models.water.P2Water4PSoft
CENTI - Static variable in class etomica.units.Prefix: Prefix indicating 10^-2 = 0.01.
centralImage(IVector) - Method in interface etomica.api.IBoundary: Determines the translation vector needed to apply a periodic-image transformation that moves the given point to an image point within the boundary (if it lies outside, in a direction subject to periodic imaging).
centralImage(IVector) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
centralImage(IVector) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
centralImage(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularNonperiodic: Returns a vector with all elements zero.
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularPeriodic
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularPore
centralImage(IVector) - Method in class etomica.space.BoundaryRectangularSlit
centralImage(IVector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
centralOrigin - Variable in class etomica.graphics.DisplayBox: Coordinate origin for central image Explicit to 2D because drawing is done to 2D image
centralOrigin - Variable in class etomica.graphics.DisplayPolytope: Coordinate origin for central image Explicit to 2D because drawing is done to 2D image
centrlFactNumt(int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: The central factorial number t(n,k) number at the indices provided.
centrlFactNumT(int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: The central factorial number T(n,k) number at the indices provided.
cErr - Variable in class etomica.potential.P2HePCKLJS
cex - Static variable in class etomica.potential.P2HydrogenPatkowski
cex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
cexIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
cFe - Variable in class etomica.meam.PotentialFeEAM_LS
cgc(int, int, int, int, int, int, int) - Method in class etomica.potential.P2HydrogenPatkowski
cgc(int, int, int, int, int, int, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
CGS - Class in etomica.units.systems: Centimeter-Gram-Second system of units.
CGS() - Constructor for class etomica.units.systems.CGS
CH2element - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
CH3element - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
cH3Type - Variable in class etomica.models.OPLS.SpeciesAceticAcid
cH3Type - Variable in class etomica.models.traPPE.SpeciesMethanol
CH4NVT - Class in etomica.AlkaneEH: CH4(TraPPE-EH) Canonical ensemble Monte Carlo simulation (NVT)
CH4NVT(Space, int, double, double, double) - Constructor for class etomica.AlkaneEH.CH4NVT
CH4NVT.Param - Class in etomica.AlkaneEH
CH_ONE - Static variable in interface etomica.graph.model.Bitmap
CH_ZERO - Static variable in interface etomica.graph.model.Bitmap
Chain - Class in etomica.virial.cluster
Chain(int) - Constructor for class etomica.virial.cluster.Chain: Constructor for Chain.
chain(int) - Static method in class etomica.virial.cluster.Standard: Returns a chain of bonds, {{0,1},{1,2},...{n-2,n-1}}
chain - Static variable in class org.jmol.script.Token
CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
chaincasesensitive - Static variable in class org.jmol.script.Token
ChainedIterator - Class in etomica.graph.iterators
ChainedIterator() - Constructor for class etomica.graph.iterators.ChainedIterator
ChainEquilibriumGraphic - Class in etomica.modules.chainequilibrium: Module for chain reaction (polymerization) using ChainEquilibriumSim as the simulation class.
ChainEquilibriumGraphic(ChainEquilibriumSim, ISpace) - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
ChainEquilibriumGraphic.Applet - Class in etomica.modules.chainequilibrium
ChainEquilibriumSim - Class in etomica.modules.chainequilibrium
ChainEquilibriumSim(ISpace) - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumSim
chainFrac - Variable in class etomica.virial.ClusterChainHS
chainFrac - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
chainFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
chainFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
chainFrac - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
chainFrac - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
chainFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
chainFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
chainFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
ChainHSMD3D - Class in etomica.simulation.prototypes
chainIterator(Iterator<Graph>) - Method in class etomica.graph.iterators.ChainedIterator
chainlength - Variable in class etomica.models.hexane.MCMoveCBMC
chainLength - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength.LengthAgent
chainLength - Variable in class etomica.modules.colloid.ColloidSim
chainLength - Variable in class etomica.modules.colloid.ConfigurationColloid
chainLength - Variable in class etomica.modules.colloid.MeterEnd2End
chainLength - Variable in class etomica.modules.colloid.NeighborListManagerColloid
chainLength - Variable in class etomica.modules.sam.Sam
chainLengthManager - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
chainLengthManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
chainNumber - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical.LengthAgent
ChainParameters(Parameters, Parameters) - Constructor for class etomica.graph.operations.UnaryChain.ChainParameters
chainPhi - Variable in class etomica.modules.sam.Sam
chainPsi - Variable in class etomica.modules.sam.Sam
CHAINS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
CHAINS - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
CHAINS - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
CHAINS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
chainTheta - Variable in class etomica.modules.sam.Sam
CHANGEABLE_MASK - Static variable in class org.jmol.util.Colix
changeableColixMap - Variable in class org.jmol.util.GData
changeableWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
changeableWV - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
changeableWV - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
changeBox() - Method in class etomica.modules.crystalviewer.LatticeEditor
changeColixArgb(short, int) - Method in class org.jmol.util.GData
characterEndA - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
characterEndB - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
characterStartA - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
characterStartB - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
charAt(int) - Method in class org.jmol.util.StringXBuilder
Charge - Class in etomica.chem.electrostatics
Charge() - Constructor for class etomica.chem.electrostatics.Charge
Charge(double) - Constructor for class etomica.chem.electrostatics.Charge
charge - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
charge - Variable in class etomica.potential.EwaldSummation.MyCharge
charge - Variable in class etomica.potential.EwaldSumMolecules.MyCharge
Charge - Class in etomica.units: The dimension for electrical charge.
charge() - Method in class etomica.units.systems.CGS
charge() - Method in class etomica.units.systems.LJ
charge() - Method in class etomica.units.systems.MKS
charge() - Method in class etomica.units.systems.UnitSystem
charge() - Method in class etomica.units.systems.UnitSystem.Sim
charge - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
charge2 - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
ChargeAgentSourceParacetamol - Class in etomica.paracetamol
ChargeAgentSourceParacetamol() - Constructor for class etomica.paracetamol.ChargeAgentSourceParacetamol
ChargeAgentSourceRPM(SpeciesWater4P, boolean) - Constructor for class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
ChargeAgentSourceTIP4PWater - Class in etomica.models.water
ChargeAgentSourceTIP4PWater() - Constructor for class etomica.models.water.ChargeAgentSourceTIP4PWater
chargeAll - Variable in class etomica.models.co2.PNCO2GCPM
chargeC - Variable in class etomica.models.co2.PNCO2GCPM
chargeC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeCC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeCC - Variable in class etomica.potential.P2CO2EMP
chargeCN - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeCO - Variable in class etomica.potential.P2CO2EMP
chargeCP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeH - Variable in class etomica.dielectric.TIP4P_NVT
chargeH - Variable in class etomica.models.water.P2Water3P
chargeH - Variable in class etomica.models.water.P2Water4P
chargeH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
chargeH - Variable in class etomica.models.water.PNWaterGCPM
chargeHH - Variable in class etomica.models.water.P2Water3P
chargeHH - Variable in class etomica.models.water.P2Water4P
chargeHH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
chargeM - Variable in class etomica.dielectric.TIP4P_NVT
chargeM - Variable in class etomica.models.water.P2Water4P
chargeM - Variable in class etomica.models.water.P2WaterTIP4PHardCore
chargeM - Variable in class etomica.models.water.PNWaterGCPM
chargeMH - Variable in class etomica.models.water.P2Water4P
chargeMH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
chargeMM - Variable in class etomica.models.water.P2Water4P
chargeMM - Variable in class etomica.models.water.P2WaterTIP4PHardCore
chargeN - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeNN - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeNP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeO - Variable in class etomica.models.co2.PNCO2GCPM
chargeO - Variable in class etomica.models.water.P2Water3P
chargeOH - Variable in class etomica.models.water.P2Water3P
chargeOO - Variable in class etomica.models.water.P2Water3P
chargeOO - Variable in class etomica.potential.P2CO2EMP
chargeP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
chargeP1 - Variable in class etomica.models.nitrogen.P2Nitrogen
chargeP1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
chargeP1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
chargeP1P1 - Variable in class etomica.models.nitrogen.P2Nitrogen
chargeP1P1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
chargeP1P1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
chargeP1P2 - Variable in class etomica.models.nitrogen.P2Nitrogen
chargeP1P2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
chargeP1P2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
chargeP2 - Variable in class etomica.models.nitrogen.P2Nitrogen
chargeP2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
chargeP2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
chargeP2P2 - Variable in class etomica.models.nitrogen.P2Nitrogen
chargeP2P2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
chargeP2P2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
chargePP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
CHbondL - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
CHbondL - Variable in class etomica.virial.ConformationAlkaneEH
check(Graph) - Method in class etomica.graph.property.FFTDecomposition
check(Graph) - Method in class etomica.graph.property.FieldNodeCountMax
check(Graph) - Method in class etomica.graph.property.HasArticulationPair
check(Graph) - Method in class etomica.graph.property.HasArticulationPoint
check(Graph) - Method in class etomica.graph.property.HasEdgeCount
check(Graph) - Method in class etomica.graph.property.HasNodalPoint
check(Graph) - Method in class etomica.graph.property.HasNoRootEdge
check(Graph) - Method in class etomica.graph.property.HasSimpleArticulationPoint
check(Graph) - Method in class etomica.graph.property.IsBiconnected
check(Graph) - Method in class etomica.graph.property.IsConnected
check(Graph) - Method in class etomica.graph.property.IsFFT
check(Graph) - Method in interface etomica.graph.property.Property
check() - Method in class etomica.util.TreeList: checks the tree for consistency of connections and ordering by sortKey.
check(Graph) - Method in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsMix2.MaxIsomorphCriteriaMixture
check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.DiscardCriteria
check(Graph) - Method in class etomica.virial.IsFFT
checkBox - Variable in class etomica.modules.clustergenerator.MyApplet
checkBox1 - Variable in class etomica.modules.clustergenerator.MyApplet
checkBox2 - Variable in class etomica.modules.clustergenerator.MyApplet
checkCarbohydrate(String) - Static method in class org.jmol.viewer.JmolConstants
CheckCBMCHexane - Class in etomica.models.hexane
CheckCBMCHexane(IBox, PotentialMaster, ISpace) - Constructor for class etomica.models.hexane.CheckCBMCHexane
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterSumHS
checkConfig(BoxCluster) - Method in interface etomica.virial.ClusterWheatley: Determines whether the configuration is zero-valued or not.
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
checkCore - Static variable in class etomica.models.co2.P2CO2H2OWheatley
checkCoreCO - Static variable in class etomica.models.co2.P2CO2H2OWheatley
checkDimensions() - Method in class etomica.lattice.CellLattice.NeighborIterator: Checks whether lattice dimensions have changed, and updates integer neighbor range if they have.
checkDimensions() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Checks the box's dimensions to make sure the number of cells is appropriate.
checkDimensions() - Method in class etomica.nbr.cell.NeighborCellManager: Checks the box's dimensions to make sure the number of cells is appropriate.
checkDimensions() - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
checkE - Static variable in class etomica.potential.P2ElectrostaticWithHardCore
checkForSimilarSites(String[], String[], IMolecularModel_SpeciesFactory[]) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
checkGraph(Graph) - Static method in class etomica.graph.operations.DecorateWertheim3SiteRho
checkIfCompatible(ModelSelectedSpecies, ModelSimulationEnvironment) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
checkIfSameSpeciesWithSimilarPotentials(IMolecularModel_SpeciesFactory, IMolecularModel_SpeciesFactory, int, int) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
checkIndexOfSpeciesSelected() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
checkme - Static variable in class etomica.virial.ClusterWheatleyPartitionScreening
checkMemory() - Static method in class org.jmol.util.Logger
checkMin() - Method in class etomica.kmc.IntegratorKMC
checkMin() - Method in class etomica.kmc.IntegratorKMCCluster
checkOHBondLength() - Method in class etomica.action.IntegratorDimerApproach
checkRing(IAtom, IAtom, int) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: this function will bond atoms a & b together
checkSet(Set<Graph>) - Static method in class etomica.graph.operations.DecorateWertheim3SiteRho
checkString(String) - Static method in class etomica.units.UnitFilter
checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
checkUnitSystemString(String) - Static method in class etomica.units.UnitFilter
chiData - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
chiData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
chiData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
chiInfo - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
chiInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
chiInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
childCount - Variable in class etomica.species.SpeciesSpheresHetero
childIndex - Variable in class etomica.atom.AtomTypeLeaf
childList - Variable in class etomica.atom.iterator.TripletInnerSequential
childList - Variable in class etomica.atom.Molecule
children - Variable in class etomica.virial.cluster.ClusterTreeNode
childTypes - Variable in class etomica.species.Species
chisq - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
chisq - Variable in class etomica.util.numerical.NonLinearCurveFitting
chiSum - Variable in class etomica.integrator.mcmove.MCMoveTracker
chiTag - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
chiTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
chiTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
chiTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
Chlorine - Class in etomica.chem.elements: Class for the Chlorine element.
Chlorine(String) - Constructor for class etomica.chem.elements.Chlorine
Chlorine(String, double) - Constructor for class etomica.chem.elements.Chlorine
choices() - Method in class etomica.action.activity.Controller.ActionStatus
choices() - Static method in class etomica.action.activity.ControllerEvent.Type
choices() - Static method in class etomica.atom.iterator.IteratorDirective.Direction
choices() - Static method in class etomica.data.AccumulatorRatioAverageCovariance
choices() - Static method in class etomica.data.AccumulatorRatioAverageCovarianceFull
choices() - Static method in class etomica.data.DataSourceUniform.LimitType
choices() - Static method in class etomica.graphics.DeviceBox.LabelType
choices() - Static method in class etomica.graphics.DisplayTextBox.LabelType
choices() - Static method in class etomica.integrator.IntegratorEvent.Type
choices() - Static method in class etomica.integrator.IntegratorMD.ThermostatType
choices() - Static method in class etomica.integrator.IntegratorNonintervalEvent.NonintervalEventType
choices() - Static method in class etomica.util.Constants.Alignment
choices() - Static method in class etomica.util.Constants.CompassDirection
choices() - Static method in class etomica.util.Constants.Direction
chooseRate() - Method in class etomica.kmc.IntegratorKMC
chooseRate() - Method in class etomica.kmc.IntegratorKMCCluster
Chop() - Constructor for class etomica.util.Function.Chop: Constructs with default cutoff value of 2 Double.MIN_VALUE.
Chop(double) - Constructor for class etomica.util.Function.Chop
chopF(MayerFunction[]) - Static method in class etomica.virial.ClusterSumStickyEF
chrg3 - Static variable in class etomica.models.water.P2WaterSzalewicz
chs() - Method in class etomica.math.Complex: Negative of this complex number (chs stands for change sign).
chType - Variable in class etomica.virial.SpeciesAnthracene3site464
chType - Variable in class etomica.virial.SpeciesAnthracene3site545
chType - Variable in class etomica.virial.SpeciesPh3site464
chType - Variable in class etomica.virial.SpeciesPh3site545
chType - Variable in class etomica.virial.SpeciesTraPPEAnthracene
chType - Variable in class etomica.virial.SpeciesTraPPENaphthalene
chType - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
Circle - Class in etomica.math.geometry: A circle in 2D.
Circle() - Constructor for class etomica.math.geometry.Circle: Creates circle with unit radius
Circle(double) - Constructor for class etomica.math.geometry.Circle: Creates circle of the given radius.
circle(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
CL_OPTION_ALLOWED_SCRIPTS - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the set of allowed scripts
CL_OPTION_ALLOWED_SCRIPTS_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_ALTERNATE_STYLESHEET - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the CSS alternate stylesheet when converting the SVG images
CL_OPTION_ALTERNATE_STYLESHEET_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_AOI - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the area of interest in the output image.
CL_OPTION_AOI_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_BACKGROUND_COLOR - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output image's background color
CL_OPTION_BACKGROUND_COLOR_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_CONSTRAIN_SCRIPT_ORIGIN - Static variable in class etomica.graph.view.rasterizer.Main: Option to determine whether scripts a constrained to the same origin as the document referencing them.
CL_OPTION_CONSTRAIN_SCRIPT_ORIGIN_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_DEFAULT_FONT_FAMILY - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the default value for the font-family CSS property when converting the SVG image
CL_OPTION_DEFAULT_FONT_FAMILY_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_DPI - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the resolution for the output image
CL_OPTION_DPI_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_HEIGHT - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output image's height
CL_OPTION_HEIGHT_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_INDEXED - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify if the PNG should be indexed.
CL_OPTION_INDEXED_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_LANGUAGE - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the user language with which SVG documents should be processed
CL_OPTION_LANGUAGE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_MAX_HEIGHT - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output image's maximum height.
CL_OPTION_MAX_HEIGHT_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_MAX_WIDTH - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output image's maximum width.
CL_OPTION_MAX_WIDTH_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_MEDIA_TYPE - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the CSS media type when converting the SVG image
CL_OPTION_MEDIA_TYPE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_MIME_TYPE - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output image's mime type
CL_OPTION_MIME_TYPE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_ONLOAD - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify that the converted SVG files should be after the dispatch of the 'onload' event.
CL_OPTION_ONLOAD_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_OUTPUT - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output directory or file
CL_OPTION_OUTPUT_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_QUALITY - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output JPEG quality
CL_OPTION_QUALITY_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_SECURITY_OFF - Static variable in class etomica.graph.view.rasterizer.Main: Option to turn off secure execution of scripts
CL_OPTION_SECURITY_OFF_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_SNAPSHOT_TIME - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify that the document should be rasterized after seeking to the specified document time.
CL_OPTION_SNAPSHOT_TIME_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_USER_STYLESHEET - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify an addition user stylesheet
CL_OPTION_USER_STYLESHEET_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_VALIDATE - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify that the converted SVG files should be validated during the conversion process.
CL_OPTION_VALIDATE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
CL_OPTION_WIDTH - Static variable in class etomica.graph.view.rasterizer.Main: Option to specify the output image's width
CL_OPTION_WIDTH_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
clash - Static variable in class org.jmol.script.Token
CLASSBASE_OPTIONS - Static variable in class org.jmol.viewer.JmolConstants
classical - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
classlist() - Static method in class etomica.units.Lister
ClassRequirement - Class in etomica.compatibility
ClathrateHarmonicFE - Class in etomica.models.clathrates
ClathrateHarmonicFE(ISpace, int[], double, double, double[], int, String, boolean, double, boolean) - Constructor for class etomica.models.clathrates.ClathrateHarmonicFE
ClathrateHarmonicFE.SimParams - Class in etomica.models.clathrates
clear() - Method in class etomica.atom.AtomArrayList
clear() - Method in class etomica.atom.DiameterHashByElement
clear() - Method in class etomica.atom.iterator.IteratorDirective: Puts directive in default state of no atoms specified, up direction, no potential criteria applied, no LRC included.
clear() - Method in class etomica.atom.MoleculeArrayList
clear() - Method in interface etomica.graph.engine.Console
clear() - Method in class etomica.graph.engine.ConsoleUI
clear(Parser.Command) - Method in class etomica.graph.engine.Interpreter
clear() - Method in class etomica.graph.model.GraphList
clear() - Method in class etomica.modules.clustergenerator.Plot: Clears the plot.
clear() - Method in class etomica.potential.P2HardBondedList.BondArrayList
clear() - Method in class etomica.util.ObjectArrayList: Removes all of the elements from this list.
clear() - Method in class org.jmol.g3d.Graphics3D
clear(int) - Method in class org.jmol.util.BitSet: Sets the bit specified by the index to false.
clear() - Method in class org.jmol.util.GData
clearAll() - Method in class org.jmol.util.BitSet: Sets all of the bits in this BitSet to false.
clearBit(int) - Method in interface etomica.graph.model.Bitmap
clearBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong: The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit bitSize() - 1 of bitmap.
clearBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit bitSize() - 1 of bitmap[size()-1].
clearBits(int, int) - Method in class org.jmol.util.BitSet: Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to false.
clearFontCache() - Method in class org.jmol.g3d.Graphics3D
clearFontCache() - Method in class org.jmol.util.GData
clearNbrs() - Method in class etomica.nbr.list.AtomNeighborLists: Clears neighbor lists, removing all listed neighbor atoms.
clearNbrs() - Method in class etomica.nbr.list.AtomPotentialList: Clears neighbor lists, resetting all flags to false (not interacting).
clearNbrs() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists: Clears neighbor lists, removing all listed neighbor molecules.
clearNbrs() - Method in class etomica.nbr.list.molecule.MoleculePotentialList: Clears neighbor lists, resetting all flags to false (not interacting).
clearRatesandEnergies() - Method in class etomica.kmc.IntegratorKMCCluster
clearTags() - Method in class etomica.data.DataInfo: Removes all tags.
clearTags() - Method in interface etomica.data.IEtomicaDataInfo: Removes all tags.
clipCode(int) - Method in class org.jmol.util.GData
clipCode3(int, int, int) - Method in class org.jmol.util.GData
ClipPlaneEditor - Class in etomica.modules.crystalviewer: Class that produces a panel with controls that presence, orientation and position of a plane that clips atoms from the display.
ClipPlaneEditor(ISimulation, LatticePlane, DisplayBox) - Constructor for class etomica.modules.crystalviewer.ClipPlaneEditor
clipPlaneEditor - Variable in class etomica.modules.crystalviewer.CrystalViewer
cliqueCheck(int, int) - Method in class etomica.virial.ClusterSumHS: Checks to see if the set |clique| is a clique separator.
cliqueCheck(int, int) - Method in class etomica.virial.ClusterWheatleyHS: Checks to see if the set |clique| is a clique separator.
cliqueCheck(int, int) - Method in class etomica.virial.ClusterWheatleyPartitionScreening: Checks to see if the set |clique| is a clique separator.
cliqueCount - Variable in class etomica.virial.ClusterSumHS
cliqueCount - Variable in class etomica.virial.ClusterWheatleyHS
cliqueCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
cliqueCountE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueCountEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueCountF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueCountNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueList - Variable in class etomica.virial.ClusterSumHS
cliqueList - Variable in class etomica.virial.ClusterWheatleyHS
cliqueList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
cliqueListE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueListEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueListF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueListNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueSet - Variable in class etomica.virial.ClusterSumHS
cliqueSet - Variable in class etomica.virial.ClusterWheatleyHS
cliqueSet - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
cliqueSetE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueSetEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueSetF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
cliqueSetNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
clone() - Method in class etomica.atom.iterator.IteratorDirective.PotentialCriterion
clone() - Method in interface etomica.space.Tensor
clone() - Method in class etomica.space1d.Tensor1D: Support of implementation of Cloneable interface.
clone() - Method in class etomica.space2d.Tensor2D: Support of implementation of Cloneable interface.
clone() - Method in class etomica.space3d.Tensor3D: Support of implementation of Cloneable interface.
clone() - Method in class etomica.spaceNd.TensorND
clone() - Method in class etomica.util.ObjectArrayList: Returns a shallow copy of this ArrayList instance.
clone() - Method in class etomica.util.ScientificFormat
clone() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Create a copy of this.
clone() - Method in class etomica.veos.bigdecimal.BigSurd: Create a deep copy.
clone() - Method in class etomica.veos.bigdecimal.Ifactor: Deep copy.
clone() - Method in class etomica.veos.bigdecimal.Rational: Create a copy.
clone() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
clone() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
clone() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
clone() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
clone() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
clone() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
clone() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
clone() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
clone() - Method in class org.jmol.util.BitSet: Cloning this BitSet produces a new BitSet that is equal to it.
close() - Method in interface etomica.graph.engine.Viewer
close() - Method in class etomica.graph.viewer.ClusterViewer
closeAlkaneView() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
closeFile() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
closeFile() - Method in class etomica.data.DataLogger
closeFile() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
closeFile() - Method in class etomica.zeolite.MSDCoordWriter
closeFW() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule: Closes file with overlap data.
closeFW() - Method in class etomica.normalmode.MeterTargetTP: Closes file with overlap data.
closeSimEnvParamView() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
closeWindow - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
CloseWindowButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBox.CloseWindowButtonListener
cluster - Variable in class etomica.modules.clustergenerator.MyApplet
cluster - Variable in class etomica.virial.MeterVirialExternalField
cluster - Variable in class etomica.virial.MeterVirialExternalFieldConfined
cluster - Variable in class etomica.virial.MeterVirialExternalFieldSW
ClusterAbstract - Interface in etomica.virial
clusterAdd - Variable in class etomica.virial.ClusterDifference
ClusterAssociation - Class in etomica.virial.cluster
ClusterAssociation() - Constructor for class etomica.virial.cluster.ClusterAssociation
clusterBD - Variable in class etomica.virial.ClusterWheatleySoft
ClusterBonds - Class in etomica.virial
ClusterBonds(int, int[][][]) - Constructor for class etomica.virial.ClusterBonds: Constructor for Cluster, with default to not using permutations (this can be changed after construction if desired).
ClusterBonds(int, int[][][], boolean) - Constructor for class etomica.virial.ClusterBonds: Constructor for Cluster.
ClusterBonds(int[][], boolean) - Constructor for class etomica.virial.ClusterBonds
ClusterBondsNonAdditive - Class in etomica.virial: Subclass of ClusterBonds capable of handling non-additive Mayer functions.
ClusterBondsNonAdditive(int, int[][][], int[][]) - Constructor for class etomica.virial.ClusterBondsNonAdditive: Construct a ClusterBondsNonAdditive of size n, using the given list of pair and multibonds.
ClusterBondsNonAdditive(int[][], int[][]) - Constructor for class etomica.virial.ClusterBondsNonAdditive
ClusterChainHS - Class in etomica.virial: This class calculates the sum of all chain and/or ring clusters for hard potentials, for which the Mayer function can take values of only -1 or 0.
ClusterChainHS(int, MayerFunction) - Constructor for class etomica.virial.ClusterChainHS: Constructs with default to perform chain-only calculation, with chainFrac = 1.0
ClusterChainHS(int, MayerFunction, boolean) - Constructor for class etomica.virial.ClusterChainHS: Constructs to perform either chain-only or ring-only calculation, as directed by doRing (true for ring-only)
ClusterChainHS(int, MayerFunction, double, double) - Constructor for class etomica.virial.ClusterChainHS: Constructs to perform linear combination of chain and ring values, with computed cluster values each weighted by given fractions, and summed to get total value
ClusterChainSoft - Class in etomica.virial: This class calculates the sum of all chain clusters.
ClusterChainSoft(int, MayerFunction) - Constructor for class etomica.virial.ClusterChainSoft
ClusterChainSoft(int, MayerFunction, boolean) - Constructor for class etomica.virial.ClusterChainSoft
ClusterCollapsedTreeNode - Class in etomica.virial.cluster
ClusterCollapsedTreeNode(int, int) - Constructor for class etomica.virial.cluster.ClusterCollapsedTreeNode
ClusterCollapsedTreeNode(ClusterTreeNode, ClusterTreeNode) - Constructor for class etomica.virial.cluster.ClusterCollapsedTreeNode
ClusterCoupledAtomFlipped - Class in etomica.virial
ClusterCoupledAtomFlipped(ClusterAbstract, ISpace) - Constructor for class etomica.virial.ClusterCoupledAtomFlipped
ClusterCoupledAtomFlipped(ClusterAbstract, ISpace, double) - Constructor for class etomica.virial.ClusterCoupledAtomFlipped
ClusterCoupledFlipped - Class in etomica.virial
ClusterCoupledFlipped(ClusterAbstract, ISpace) - Constructor for class etomica.virial.ClusterCoupledFlipped: cluster must have caching disabled
ClusterCoupledFlipped(ClusterAbstract, ISpace, double) - Constructor for class etomica.virial.ClusterCoupledFlipped: cluster must have caching disabled configurations will be flipped when the minimum distance between any two molecules exceeds minFlipDistance.
ClusterCoupledFlippedPartial - Class in etomica.virial
ClusterCoupledFlippedPartial(ClusterAbstract, ISpace, int[][]) - Constructor for class etomica.virial.ClusterCoupledFlippedPartial
clusterCriteria - Variable in class etomica.virial.ClusterSumAssociation
ClusterDiagram - Class in etomica.virial.cluster: Holds information about a cluster diagram, including the bonds, root points, and score.
ClusterDiagram(int, int) - Constructor for class etomica.virial.cluster.ClusterDiagram: Constructs a cluster having numBody points of which numRootPoints are root points, with bonds between each pair of points (full star).
ClusterDiagram(int, int, int[][]) - Constructor for class etomica.virial.cluster.ClusterDiagram: Constructs a cluster having numBody points of which numRootPoints are root points, with bonds as given by the array bonds.
ClusterDiagram(int, int, int[][], Rational) - Constructor for class etomica.virial.cluster.ClusterDiagram
ClusterDiagram(ClusterDiagram) - Constructor for class etomica.virial.cluster.ClusterDiagram: Creates a copy of the given cluster
ClusterDiagramTree - Class in etomica.virial.cluster: Holds information about a cluster diagram, including the bonds, root points, and score.
ClusterDiagramTree(int, int) - Constructor for class etomica.virial.cluster.ClusterDiagramTree: Constructs a cluster having numBody points and numRootPoints root points.
ClusterDifference - Class in etomica.virial: This class holds multiple clusters and returns the value from one minus the average value from the others.
ClusterDifference(ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.ClusterDifference
ClusterExchange - Class in etomica.virial
ClusterExchange(IPotentialAtomic) - Constructor for class etomica.virial.ClusterExchange
ClusterGenerator - Class in etomica.virial.cluster: Generates all clusters matching certain criteria.
ClusterGenerator(ClusterDiagram) - Constructor for class etomica.virial.cluster.ClusterGenerator
ClusterICPYC - Class in etomica.virial: Cluster class that computes the correction to the ICPY (incrementally corrected Percus-Yevick) formulation.
ClusterICPYC(int, MayerFunction) - Constructor for class etomica.virial.ClusterICPYC
clusterMultiBD - Variable in class etomica.virial.ClusterWheatleyMultibody
ClusterOperations - Class in etomica.virial.cluster
ClusterOperations() - Constructor for class etomica.virial.cluster.ClusterOperations
ClusterPanel - Class in etomica.modules.clustergenerator
ClusterPanel(ClusterDiagram, boolean, boolean, boolean, boolean, boolean) - Constructor for class etomica.modules.clustergenerator.ClusterPanel
ClusterPY - Class in etomica.virial
ClusterPY(int, MayerFunction) - Constructor for class etomica.virial.ClusterPY
clusterRadius - Variable in class etomica.dimer.SimDimerMEAMGB
clusters - Variable in class etomica.virial.ClusterSum
clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
clusters - Variable in class etomica.virial.MeterVirial
clusters - Variable in class etomica.virial.MeterVirialBD
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapRho
clusters - Variable in class etomica.virial.MeterVirialExternalFieldRho
clusters - Variable in class etomica.virial.MeterVirialSWWE
ClusterSinglyConnected - Class in etomica.virial: This class calculates the sum of all tree clusters using an adaptation of Wheatley's recursive formulation.
ClusterSinglyConnected(int, MayerFunction) - Constructor for class etomica.virial.ClusterSinglyConnected
clusterSubtract - Variable in class etomica.virial.ClusterDifference
ClusterSum - Class in etomica.virial
ClusterSum(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSum: Constructor for ClusterSum.
ClusterSumAssociation - Class in etomica.virial: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's double attraction-site model, hyper-point diagram 2 F-bond, 1 f_R bond diagram
ClusterSumAssociation(ClusterBonds[], double[], MayerFunction[], ClusterSumAssociation.ClusterCriteria) - Constructor for class etomica.virial.ClusterSumAssociation: Constructor for ClusterSum.
ClusterSumAssociation.ClusterCriteria - Interface in etomica.virial
ClusterSumEF - Class in etomica.virial
ClusterSumEF(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumEF: Constructs a Cluster sum of the given cluster and weights.
ClusterSumExternalField - Class in etomica.virial
ClusterSumExternalField(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumExternalField
ClusterSumHS - Class in etomica.virial: This class calculates the sum of all biconnected clusters for hard spheres.
ClusterSumHS(ClusterBonds[], double[], MayerFunction) - Constructor for class etomica.virial.ClusterSumHS
ClusterSumIC - Class in etomica.virial
ClusterSumIC(ClusterBonds[], double[], MayerFunction[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumIC
ClusterSumIC.FR2 - Class in etomica.virial
ClusterSumMultibody - Class in etomica.virial: Cluster class capable of computing multibody (up to 6th order) contributions to diagrams.
ClusterSumMultibody(ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterSumMultibody
ClusterSumMultibodyShell - Class in etomica.virial
ClusterSumMultibodyShell(ClusterSumMultibody, ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterSumMultibodyShell: Constructs a cluster (shell) that depends on another ClusterSumMultibody instance (the core) to do the actual work of calculating all the f values.
ClusterSumNonAdditiveTrimerEnergy - Class in etomica.virial
ClusterSumNonAdditiveTrimerEnergy(ClusterBonds[], double[], MayerFunction[], Potential) - Constructor for class etomica.virial.ClusterSumNonAdditiveTrimerEnergy: Adapted by Kate from ClusterSumPolarizable (simplification for nonadditive trimer energy only).
ClusterSumPolarizable - Class in etomica.virial
ClusterSumPolarizable(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizable: Constructor for ClusterSum.
ClusterSumPolarizableWertheimProduct - Class in etomica.virial
ClusterSumPolarizableWertheimProduct(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct: Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumPolarizableWertheimProduct4Pt - Class in etomica.virial
ClusterSumPolarizableWertheimProduct4Pt(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt: Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumPolarizableWertheimProduct4PtFinal - Class in etomica.virial
ClusterSumPolarizableWertheimProduct4PtFinal(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal: Constructor for ClusterSum for Wertheim diagram including multi body term.
ClusterSumShell - Class in etomica.virial
ClusterSumShell(ClusterSum, ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumShell: Constructs a cluster (shell) that depends on another ClusterSum instance (the core) to do the actual work of calculating all the f values.
ClusterSumStickyEF - Class in etomica.virial
ClusterSumStickyEF(ClusterBonds[], double[], MayerFunction[], ClusterSumStickyEF[], IRandom) - Constructor for class etomica.virial.ClusterSumStickyEF
ClusterSumStickyEF(ClusterSumEF, ClusterSumStickyEF[], IRandom) - Constructor for class etomica.virial.ClusterSumStickyEF
ClusterTree - Class in etomica.virial
ClusterTree(ClusterDiagramTree, MayerFunction[]) - Constructor for class etomica.virial.ClusterTree
ClusterTreeBonds - Class in etomica.virial
ClusterTreeBonds() - Constructor for class etomica.virial.ClusterTreeBonds
ClusterTreeEF - Class in etomica.virial
ClusterTreeEF(ClusterDiagramTree, MayerFunction[]) - Constructor for class etomica.virial.ClusterTreeEF
ClusterTreeNode - Class in etomica.virial.cluster
ClusterTreeNode(int) - Constructor for class etomica.virial.cluster.ClusterTreeNode
ClusterViewer - Class in etomica.graph.viewer
ClusterWeight - Interface in etomica.virial
ClusterWeight.Factory - Interface in etomica.virial
ClusterWeightAbs - Class in etomica.virial
ClusterWeightAbs(ClusterAbstract) - Constructor for class etomica.virial.ClusterWeightAbs
clusterWeights - Variable in class etomica.virial.ClusterSum
clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
ClusterWeightSumWall - Class in etomica.virial
ClusterWeightSumWall(ClusterWeightSumWall.DataSourceClusterWall, int) - Constructor for class etomica.virial.ClusterWeightSumWall
ClusterWeightSumWall.DataSourceClusterWall - Interface in etomica.virial
ClusterWeightUmbrella - Class in etomica.virial: Umbrella cluster weight wrapper function.
ClusterWeightUmbrella(ClusterAbstract[]) - Constructor for class etomica.virial.ClusterWeightUmbrella: Contructs an umbrella cluster from the given clusters.
ClusterWheatley - Interface in etomica.virial
clusterWheatleyBDBD - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
ClusterWheatleyExtendSW - Class in etomica.virial
ClusterWheatleyExtendSW(int, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyExtendSW
ClusterWheatleyHS - Class in etomica.virial: This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleyHS(int, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyHS
ClusterWheatleyHS.AllSigs - Class in etomica.virial
ClusterWheatleyMultibody - Class in etomica.virial: This class uses Wheatley's recursion approach to calculating all biconnected diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterWheatleyMultibody
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive) - Constructor for class etomica.virial.ClusterWheatleyMultibody
ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], double) - Constructor for class etomica.virial.ClusterWheatleyMultibody
ClusterWheatleyMultibodyBD - Class in etomica.virial: This class uses Wheatley's recursion approach to calculating all biconnected diagrams, but adds in non-additive contributions.
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive[], int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
ClusterWheatleyMultibodyMix - Class in etomica.virial: This class uses Wheatley's recursion approach to calculating all biconnected diagrams for a mixture, but adds in 3-body contributions.
ClusterWheatleyMultibodyMix(int, int[], MayerFunction[][], MayerFunctionNonAdditive[][][], double, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyMix: Constructs a cluster capable of handling mixtures of nonadditive molecules.
ClusterWheatleyPartitionScreening - Class in etomica.virial: This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleyPartitionScreening(int, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyPartitionScreening
ClusterWheatleyPartitionScreening(int, MayerFunction, int) - Constructor for class etomica.virial.ClusterWheatleyPartitionScreening
ClusterWheatleyPartitionScreening.FrequencyCounter - Class in etomica.virial
ClusterWheatleySoft - Class in etomica.virial: This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleySoft(int, MayerFunction, double) - Constructor for class etomica.virial.ClusterWheatleySoft
ClusterWheatleySoftBD - Class in etomica.virial: This class calculates the sum of all biconnected clusters using Wheatley's recursive formulation.
ClusterWheatleySoftBD(int, MayerFunction, int) - Constructor for class etomica.virial.ClusterWheatleySoftBD
ClusterWheatleySoftBDMix - Class in etomica.virial: Cluster class using Whealtey's recursion with BigDecimal to handle mixtures.
ClusterWheatleySoftBDMix(int, int[], MayerFunction[][], int) - Constructor for class etomica.virial.ClusterWheatleySoftBDMix
ClusterWheatleySoftMix - Class in etomica.virial: Cluster class using Whealtey's recursion to handle mixtures.
ClusterWheatleySoftMix(int, int[], MayerFunction[][], double) - Constructor for class etomica.virial.ClusterWheatleySoftMix
cm - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
cm2ndD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
Cmax - Variable in class etomica.meam.ParameterSetMEAM
Cmin - Variable in class etomica.meam.ParameterSetMEAM
cmtoau - Static variable in class etomica.potential.P2WaterPotentialsJankowski
cmzFix - Static variable in class etomica.models.water.P2WaterSzalewicz
cn - Variable in class etomica.potential.P3HydrogenManzhos
CO - Variable in class etomica.models.co2.P2CO2H2OWheatley
coef - Variable in class etomica.potential.P2HydrogenHinde
coef - Variable in class etomica.potential.P2HydrogenHindeAtomic
Coefficient - Interface in etomica.graph.model
coefficient() - Method in interface etomica.graph.model.Graph
coefficient() - Method in class etomica.graph.model.impl.GraphImpl
coefficient - Variable in class etomica.virial.cluster.ClusterTreeNode
coefficient_fourier - Variable in class etomica.potential.EwaldSumMolecules
CoefficientImpl - Class in etomica.graph.model.impl
CoefficientImpl(int) - Constructor for class etomica.graph.model.impl.CoefficientImpl
CoefficientImpl(int, int) - Constructor for class etomica.graph.model.impl.CoefficientImpl
CoefficientImpl(int, int, double) - Constructor for class etomica.graph.model.impl.CoefficientImpl
coefficients - Variable in class etomica.normalmode.WaveVectorFactory1D
coefficients - Variable in class etomica.normalmode.WaveVectorFactory2D
coefficients - Variable in class etomica.normalmode.WaveVectorFactoryFcc
coefficients - Variable in class etomica.normalmode.WaveVectorFactorySimple
coefficients - Variable in class etomica.virial.MayerFunctionProductGeneral
coefficients - Variable in class etomica.virial.MayerFunctionSum
coefficients - Variable in class etomica.virial.MayerFunctionSumGeneral
coeffQ(int) - Method in class etomica.veos.QSeries: Computes coefficients of the polynomial in volume for Q for the given N.
coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
Colix - Class in org.jmol.util: Implements a color index model using a colix as a COLor IndeX.
Colix() - Constructor for class org.jmol.util.Colix
colix - Variable in class org.jmol.util.MeshSurface
colixBack - Variable in class org.jmol.util.MeshSurface
colixCurrent - Variable in class org.jmol.util.GData
collapse() - Method in class etomica.virial.cluster.ClusterDiagramTree
collapseBlocks() - Method in class etomica.data.AccumulatorAverageCollapsing
collapseData(double) - Method in class etomica.util.HistogramCollapsing: Collapses existing data and expands x range sufficiently so that the given x value is within the range of the histogram.
collapseData() - Method in class etomica.util.HistoryCollapsing
collapseData() - Method in class etomica.util.HistoryCollapsingAverage
collapseData() - Method in class etomica.util.HistoryCollapsingDiscard
CollectionBondedPotentialAlcohols - Class in etomica.virial.GUI.components
CollectionBondedPotentialAlcohols() - Constructor for class etomica.virial.GUI.components.CollectionBondedPotentialAlcohols
CollectionBondedPotentialAlkanes - Class in etomica.virial.GUI.components
CollectionBondedPotentialAlkanes(int) - Constructor for class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
CollectionPotentialAtomicLike - Class in etomica.virial.GUI.components
CollectionPotentialAtomicLike(int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialAtomicLike
CollectionPotentialAtomicUnlike - Class in etomica.virial.GUI.components
CollectionPotentialAtomicUnlike(int, int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
CollectionPotentialMolecularLike - Class in etomica.virial.GUI.components
CollectionPotentialMolecularLike(int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialMolecularLike
CollectionPotentialMolecularUnlike - Class in etomica.virial.GUI.components
CollectionPotentialMolecularUnlike(int, int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
colliderAgent - Variable in class etomica.integrator.IntegratorHard
colliderAgent() - Method in class etomica.integrator.IntegratorHard
colliderColor - Variable in class etomica.graphics.ColorSchemeColliders: Color applied to the downList atom of the colliding pair
collisionAction(IntegratorHard.Agent) - Method in class etomica.data.DataSourceTensorVirialHard: Sums contribution to virial for each collision.
collisionAction(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHard: Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHardTensor
collisionAction(IntegratorHard.Agent) - Method in interface etomica.integrator.IntegratorHard.CollisionListener
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis: Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.catalysis.InteractionTracker
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile: Sums contribution to virial for each collision.
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.mu.DataSourceWallPressureMu: Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.osmosis.MeterOsmoticPressure
collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.pistoncylinder.DataSourceWallPressure: Implementation of CollisionListener interface Adds collision virial (from potential) to accumulator
collisionCount - Variable in class etomica.integrator.IntegratorHard
collisionDiameter - Variable in class etomica.potential.P2HardSphere: Separation at which spheres first overlap
collisionHandlerDown - Variable in class etomica.integrator.IntegratorHard
collisionHandlerUp - Variable in class etomica.integrator.IntegratorHard
CollisionHandlerUp() - Constructor for class etomica.integrator.IntegratorHard.CollisionHandlerUp
collisionListenerHead - Variable in class etomica.integrator.IntegratorHard
collisionPartner - Variable in class etomica.integrator.IntegratorHard.Agent
collisionPartner() - Method in class etomica.integrator.IntegratorHard.Agent
collisionPotential - Variable in class etomica.integrator.IntegratorHard.Agent
collisionTime() - Method in class etomica.integrator.IntegratorHard.Agent: Accessor method for the time to next collision of this atom
collisionTime(IAtomList, double) - Method in class etomica.modules.adsorption.P1Wall
collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBonding: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellSurface: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: Computes next time of collision of the two atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: Computes next time of collision of the two atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P1Wall
collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P2HardSphereMC: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P2SquareWellMonomer: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.mu.P1MagicWall
collisionTime(IAtomList, double) - Method in class etomica.modules.mu.P2SquareWellOneSide: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.osmosis.P1HardWall
collisionTime(IAtomList, double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded: Computes next time of collision of the two atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
collisionTime(IAtomList, double) - Method in class etomica.normalmode.P2XOrder
collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardBoundary
collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardMovingBoundary
collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardPeriodic
collisionTime(IAtomList, double) - Method in class etomica.potential.P2DoubleWell: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardAssociation: Computes the next time of collision of the given atomPair assuming free flight.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardBond: Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardBondedList
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardSphere: Time to collision of pair, assuming free-flight kinematics
collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardWrapper
collisionTime(IAtomList, double) - Method in class etomica.potential.P2Ideal: Returns Double.POSITIVE_INFINITY.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableBond
collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableSphere: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableSquareWell: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2SquareWell: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2SquareWellRobust: Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
collisionTime(IAtomList, double) - Method in class etomica.potential.P2Tether: Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
collisionTime(IAtomList, double) - Method in interface etomica.potential.PotentialHard: Computes the time of collision of the given atom(s) with the hard potential, assuming no intervening collisions.
collisionTimeStep - Variable in class etomica.integrator.IntegratorHard
collisionValue(IntegratorHard.Agent) - Method in class etomica.data.DataSourceTensorVirialHard: Contribution to the virial from the most recent collision of the given pair/potential.
collisionValue(IntegratorHard.Agent) - Method in interface etomica.data.meter.DataSourceCollisional
collisionValue(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHard: Implementation of Meter.MeterCollisional interface.
colloidDensityProfileMeter - Variable in class etomica.modules.colloid.ColloidGraphic
ColloidGraphic - Class in etomica.modules.colloid: Colloid module app.
ColloidGraphic(ColloidSim, Space) - Constructor for class etomica.modules.colloid.ColloidGraphic
ColloidGraphic.Applet - Class in etomica.modules.colloid
ColloidGraphic.GraftAction - Class in etomica.modules.colloid
ColloidGraphic.WallRangeModifier - Class in etomica.modules.colloid
colloidMonomerBondManager - Variable in class etomica.modules.colloid.ColloidSim
colloidMonomerBondManager - Variable in class etomica.modules.colloid.ConfigurationColloid
ColloidSim - Class in etomica.modules.colloid: Colloid simulation.
ColloidSim(Space) - Constructor for class etomica.modules.colloid.ColloidSim
ColloidSim.CriterionNone - Class in etomica.modules.colloid
color - Variable in class etomica.association.ColorSchemeSmer.ColorAgent
color - Variable in class etomica.graph.operations.Decorate.DecorateParameters
color() - Method in class etomica.graph.operations.DeleteEdgeParameters
color() - Method in class etomica.graph.operations.DifByConstant.DifByConstantParameters
color() - Method in class etomica.graph.operations.DifParameters
color - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
color - Variable in class g3dsys.images.Bond
color - Static variable in class org.jmol.script.Token
color1 - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
COLOR_0 - Static variable in interface etomica.graph.model.Metadata
COLOR_1 - Static variable in interface etomica.graph.model.Metadata
COLOR_10 - Static variable in interface etomica.graph.model.Metadata
COLOR_11 - Static variable in interface etomica.graph.model.Metadata
COLOR_12 - Static variable in interface etomica.graph.model.Metadata
COLOR_2 - Static variable in interface etomica.graph.model.Metadata
COLOR_3 - Static variable in interface etomica.graph.model.Metadata
COLOR_4 - Static variable in interface etomica.graph.model.Metadata
COLOR_5 - Static variable in interface etomica.graph.model.Metadata
COLOR_6 - Static variable in interface etomica.graph.model.Metadata
COLOR_7 - Static variable in interface etomica.graph.model.Metadata
COLOR_8 - Static variable in interface etomica.graph.model.Metadata
COLOR_9 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_0 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_1 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_2 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_3 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_4 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_5 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_6 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_7 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_8 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_9 - Static variable in interface etomica.graph.model.Metadata
COLOR_CODE_DEFAULT - Static variable in interface etomica.graph.model.Metadata
COLOR_CODES - Static variable in interface etomica.graph.model.Metadata
COLOR_MAP - Static variable in interface etomica.graph.model.Metadata
ColorAgent() - Constructor for class etomica.association.ColorSchemeSmer.ColorAgent
colorAllAtoms() - Method in interface etomica.graphics.ColorSchemeCollective: Determine color of all atoms.
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeCollectiveAgent
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeCoordination
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeNeighbor
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeNeighborCell
colorAllAtoms() - Method in class etomica.graphics.ColorSchemeOverlap
colorAllAtoms() - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
colorAllAtoms() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
colorAllAtoms() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
colorAllAtoms() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
colorCounts - Variable in class etomica.graph.model.comparators.ComparatorNodeColors
colorMaps - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
colorNew() - Method in class etomica.graph.operations.DifByConstant.DifByConstantParameters
ColorOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.ColorOptionHandler
colorPointFromInt(int, Point3f) - Static method in class org.jmol.util.ColorUtil
colorPointFromInt2(int) - Static method in class org.jmol.util.ColorUtil
colorPointFromString(String, Point3f) - Static method in class org.jmol.util.ColorUtil
colorPtToInt(Point3f) - Static method in class org.jmol.util.ColorUtil
colorrasmol - Static variable in class org.jmol.script.Token
colors - Variable in class etomica.association.ColorSchemeSmerByLength
colors - Variable in class etomica.graph.model.comparators.ComparatorNodeColors
COLORS - Static variable in interface etomica.graph.model.Metadata
colors - Variable in class etomica.graphics.ColorSchemeOverlap
colors - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
ColorScheme - Class in etomica.graphics: Class that defines the algorithm used to determine atoms colors when drawn to DisplayBox.
ColorScheme() - Constructor for class etomica.graphics.ColorScheme
ColorScheme(Color) - Constructor for class etomica.graphics.ColorScheme
colorScheme - Variable in class etomica.graphics.DisplayBox
colorScheme - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
ColorScheme.Simple - Class in etomica.graphics: Colors all atoms with baseColor.
ColorSchemeByType - Class in etomica.graphics: Colors the atom according to the color given by its type field.
ColorSchemeByType(ISimulation) - Constructor for class etomica.graphics.ColorSchemeByType
ColorSchemeCell - Class in etomica.graphics
ColorSchemeCell(PotentialMasterNbr, IRandom, IBox) - Constructor for class etomica.graphics.ColorSchemeCell
ColorSchemeCollective - Interface in etomica.graphics
ColorSchemeCollectiveAgent - Class in etomica.graphics: Parent class for color schemes that are best implemented by attaching colors to all atoms at once, rather than determining the color of each as it is drawn.
ColorSchemeCollectiveAgent(IBox) - Constructor for class etomica.graphics.ColorSchemeCollectiveAgent
ColorSchemeColliders - Class in etomica.graphics: This colorScheme acts to color differently the two atoms that are scheduled to collide next.
ColorSchemeColliders(IntegratorHard) - Constructor for class etomica.graphics.ColorSchemeColliders
ColorSchemeCoordination - Class in etomica.graphics
ColorSchemeCoordination(ISimulation, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeCoordination
ColorSchemeDisplacement(CoordinateDefinition, ISpace, HSNPT.ActionSummer) - Constructor for class etomica.normalmode.HSNPT.ColorSchemeDisplacement
ColorSchemeDropletSurface - Class in etomica.modules.droplet
ColorSchemeDropletSurface(AtomFilterCollective) - Constructor for class etomica.modules.droplet.ColorSchemeDropletSurface
ColorSchemeLiquidVapor - Class in etomica.modules.droplet
ColorSchemeLiquidVapor(AtomFilterCollective) - Constructor for class etomica.modules.droplet.ColorSchemeLiquidVapor
ColorSchemeNeighbor - Class in etomica.graphics: Color atoms based on being neighbors of the reference atom
ColorSchemeNeighbor(ISimulation, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeNeighbor
ColorSchemeNeighborCell - Class in etomica.graphics: Colors atoms based on being in a neighboring cell to a reference atom.
ColorSchemeNeighborCell(ISimulation, PotentialMasterNbr, IBox, int) - Constructor for class etomica.graphics.ColorSchemeNeighborCell
ColorSchemeNull - Class in etomica.graphics: Does nothing at any time to set atom's color, leaving color to be set to default value.
ColorSchemeNull() - Constructor for class etomica.graphics.ColorSchemeNull
ColorSchemeOverlap - Class in etomica.graphics: Color atoms based on how many overlaps they have with their neighbors
ColorSchemeOverlap(ISpace, PotentialMasterList, IBox) - Constructor for class etomica.graphics.ColorSchemeOverlap
colorSchemeOverlap - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
ColorSchemePlane - Class in etomica.modules.crystalviewer: Colors atoms according to whether or not they are in a plane, as determined by the inPlane method of a Plane instance.
ColorSchemePlane(LatticePlane) - Constructor for class etomica.modules.crystalviewer.ColorSchemePlane
ColorSchemePlane(LatticePlane, Color, Color) - Constructor for class etomica.modules.crystalviewer.ColorSchemePlane
ColorSchemeRadical - Class in etomica.modules.catalysis
ColorSchemeRadical(ISimulation, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.ColorSchemeRadical
ColorSchemeRadical - Class in etomica.modules.chainequilibrium
ColorSchemeRadical(ISimulation, AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.ColorSchemeRadical
ColorSchemeRadical.LengthAgent - Class in etomica.modules.chainequilibrium
ColorSchemeRandom - Class in etomica.graphics
ColorSchemeRandom(IBox, IRandom) - Constructor for class etomica.graphics.ColorSchemeRandom
ColorSchemeRandomByMolecule - Class in etomica.graphics
ColorSchemeRandomByMolecule(ISimulation, IBox, IRandom) - Constructor for class etomica.graphics.ColorSchemeRandomByMolecule
colorSchemeScaled - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
ColorSchemeScaledOverlap - Class in etomica.normalmode.nptdemo: Color atoms based on being neighbors of the reference atom
ColorSchemeScaledOverlap(ISpace, PotentialMasterList, CoordinateDefinition) - Constructor for class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
ColorSchemeSmer - Class in etomica.association: Color scheme for smer association.
ColorSchemeSmer(IAssociationHelper, IBox, IRandom) - Constructor for class etomica.association.ColorSchemeSmer
ColorSchemeSmer.ColorAgent - Class in etomica.association
ColorSchemeSmerByLength - Class in etomica.association: Color scheme for smer association.
ColorSchemeSmerByLength(IAssociationHelper, IRandom) - Constructor for class etomica.association.ColorSchemeSmerByLength
ColorSchemeStepWise - Class in etomica.modules.chainequilibrium: Color scheme for stepwise growth, based on the AtomType (alcohol vs.
ColorSchemeStepWise(ISimulation, AtomLeafAgentManager) - Constructor for class etomica.modules.chainequilibrium.ColorSchemeStepWise
ColorSchemeTemperature - Class in etomica.graphics: Colors atoms according to their kinetic energy.
ColorSchemeTemperature() - Constructor for class etomica.graphics.ColorSchemeTemperature: Constructs with default low of 200K and high of 400K.
ColorSchemeTemperature(double, double) - Constructor for class etomica.graphics.ColorSchemeTemperature
colorTriadToInt(float, float, float) - Static method in class org.jmol.util.ColorUtil
ColorUtil - Class in org.jmol.util
ColorUtil() - Constructor for class org.jmol.util.ColorUtil
cols - Variable in class etomica.graphics.DeviceButtonGroup
columnHeaders - Variable in class etomica.graphics.DisplayTable
columnInfoFactories - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
columnNames - Variable in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
columnNames - Variable in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
columnNames - Variable in class etomica.virial.GUI.models.ModelPotParamDisplayTable
com - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
com - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
com - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
com - Variable in class etomica.virial.MCMoveClusterRingRegrow
com - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
com - Variable in class etomica.virial.MCMoveClusterRingScale
com0 - Variable in class etomica.models.water.OrientationCalcWater3P
com0 - Variable in class etomica.models.water.OrientationCalcWater4P
com0 - Variable in class etomica.models.water.P2WaterSzalewicz
com0 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
com0 - Variable in class etomica.potential.P2HydrogenHinde
com0 - Variable in class etomica.potential.P2HydrogenHindeAtomic
com0 - Variable in class etomica.potential.P2HydrogenHindePatkowski
com0 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
com0 - Variable in class etomica.potential.P2HydrogenPatkowski
com0 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
com0 - Variable in class etomica.virial.MCMoveClusterRingRegrow
com0 - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
com1 - Variable in class etomica.models.nitrogen.P2Nitrogen
com1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
com1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
com1 - Variable in class etomica.models.water.P2Water4P
com1 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
com1 - Variable in class etomica.potential.P2HydrogenHinde
com1 - Variable in class etomica.potential.P2HydrogenHindeAtomic
com1 - Variable in class etomica.potential.P2HydrogenHindePatkowski
com1 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
com1 - Variable in class etomica.potential.P2HydrogenPatkowski
com1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
com2 - Variable in class etomica.models.nitrogen.P2Nitrogen
com2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
com2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
com2 - Variable in class etomica.models.water.P2Water4P
com3 - Variable in class etomica.models.water.P2WaterSzalewicz
CombinationIterator - Class in etomica.math.discrete: Iterator that returns different combinations of n integers taken k at a time.
CombinationIterator(int, int) - Constructor for class etomica.math.discrete.CombinationIterator: Constructor for CombinationIterator.
combinationProbability - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
combineAB - Variable in class etomica.graph.operations.MaxIsomorphWertheim
CombineABSite - Class in etomica.graph.operations: Operation that attempts to change bonds in a graph so that equivalent graphs in a set can be combined.
CombineABSite() - Constructor for class etomica.graph.operations.CombineABSite
CombineABSite.CombineABSiteParameters - Class in etomica.graph.operations
CombineABSiteParameters(List<Character>, List<Character>) - Constructor for class etomica.graph.operations.CombineABSite.CombineABSiteParameters
combineGraphs(Graph, Graph) - Method in class etomica.graph.iterators.CartesianIterator
combineGraphs(Graph, Graph) - Method in class etomica.graph.iterators.PartitionedIterator
combineLonelyNodes - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
combinePermutations(byte[], byte[]) - Method in class etomica.graph.iterators.CartesianPermutator
comHack - Static variable in class etomica.potential.P2WaterPotentialsJankowski
comHackDist - Static variable in class etomica.potential.P2WaterPotentialsJankowski
COMMAND_CLEAR - Static variable in interface etomica.graph.engine.Parser
COMMAND_DISPLAY - Static variable in interface etomica.graph.engine.Parser
COMMAND_DROP - Static variable in interface etomica.graph.engine.Parser
COMMAND_LIST - Static variable in interface etomica.graph.engine.Parser
COMMAND_PRINT - Static variable in interface etomica.graph.engine.Parser
COMMAND_QUIT - Static variable in interface etomica.graph.engine.Parser
COMMAND_READ - Static variable in interface etomica.graph.engine.Parser
COMMAND_READDB - Static variable in interface etomica.graph.engine.Parser
COMMAND_RUN - Static variable in interface etomica.graph.engine.Parser
COMMAND_SAVE - Static variable in interface etomica.graph.engine.Parser
COMMAND_SET - Static variable in interface etomica.graph.engine.Parser
COMMAND_SUMMARY - Static variable in interface etomica.graph.engine.Parser
COMMAND_WRITE - Static variable in interface etomica.graph.engine.Parser
COMMAND_WRITEDB - Static variable in interface etomica.graph.engine.Parser
CommandImpl - Class in etomica.graph.engine.impl
CommandImpl(String) - Constructor for class etomica.graph.engine.impl.CommandImpl
CommandPropertyValueImpl - Class in etomica.graph.engine.impl
CommandPropertyValueImpl(String, Parser.Property, Parser.Value) - Constructor for class etomica.graph.engine.impl.CommandPropertyValueImpl
CommandValueImpl - Class in etomica.graph.engine.impl
CommandValueImpl(String, Parser.Value) - Constructor for class etomica.graph.engine.impl.CommandValueImpl
CommandVariableImpl - Class in etomica.graph.engine.impl
CommandVariableImpl(String, Parser.Variable) - Constructor for class etomica.graph.engine.impl.CommandVariableImpl
CommandVariableValueImpl - Class in etomica.graph.engine.impl
CommandVariableValueImpl(String, Parser.Variable, Parser.Value) - Constructor for class etomica.graph.engine.impl.CommandVariableValueImpl
comOld - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
comOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
comparableInstance(Bitmap) - Method in interface etomica.graph.model.Bitmap: Returns a bitmap instance with the same number of bits as this bitmap.
comparableInstance(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
comparator - Variable in class etomica.graph.model.GraphList
comparator - Variable in class etomica.graph.property.FFTDecomposition
comparator - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
ComparatorBiConnected - Class in etomica.graph.model.comparators
ComparatorBiConnected() - Constructor for class etomica.graph.model.comparators.ComparatorBiConnected
ComparatorChain - Class in etomica.graph.model.comparators: Comparator class that can chain together a list of comparators.
ComparatorChain() - Constructor for class etomica.graph.model.comparators.ComparatorChain
comparatorDirections - Variable in class etomica.graph.model.comparators.ComparatorChain
ComparatorNodeColors - Class in etomica.graph.model.comparators: Compares based on graph factors (when available) or node colors.
ComparatorNodeColors() - Constructor for class etomica.graph.model.comparators.ComparatorNodeColors
ComparatorNodeColors(char[]) - Constructor for class etomica.graph.model.comparators.ComparatorNodeColors
ComparatorNumEdges - Class in etomica.graph.model.comparators
ComparatorNumEdges() - Constructor for class etomica.graph.model.comparators.ComparatorNumEdges
ComparatorNumFieldNodes - Class in etomica.graph.model.comparators
ComparatorNumFieldNodes() - Constructor for class etomica.graph.model.comparators.ComparatorNumFieldNodes
ComparatorNumFieldNodesExchange() - Constructor for class etomica.virial.cluster.VirialDiagrams.ComparatorNumFieldNodesExchange
ComparatorNumFieldNodesExchange() - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ComparatorNumFieldNodesExchange
ComparatorNumNodes - Class in etomica.graph.model.comparators
ComparatorNumNodes() - Constructor for class etomica.graph.model.comparators.ComparatorNumNodes
ComparatorNumRootNodes - Class in etomica.graph.model.comparators
ComparatorNumRootNodes() - Constructor for class etomica.graph.model.comparators.ComparatorNumRootNodes
comparators - Variable in class etomica.graph.model.comparators.ComparatorChain
ComparatorStrand() - Constructor for class etomica.graph.property.FFTDecomposition.ComparatorStrand
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorBiConnected
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorChain
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNodeColors
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumEdges
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumFieldNodes
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumNodes
compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumRootNodes
compare(Object, Object) - Method in class etomica.graph.property.FFTDecomposition.ComparatorStrand
compare(Graph, Graph) - Method in class etomica.virial.cluster.VirialDiagrams.ComparatorNumFieldNodesExchange
compare(Graph, Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.ComparatorNumFieldNodesExchange
compare(DoubleRange, DoubleRange) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined.RangeComparator
compare(ScriptVariable, ScriptVariable) - Method in class org.jmol.script.ScriptVariable.Sort
compare(Object[], Object[]) - Method in class org.jmol.util.Eigen.EigenSort
comparedWV - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
comparedWV - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
comparedWV - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
comparedWV - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
comparedWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
comparedWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
comparedWV - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
compareTo(IAtomType) - Method in class etomica.atom.AtomTypeLeaf
compareTo(Feature) - Method in class etomica.compatibility.Feature
compareTo(int, Feature) - Method in class etomica.compatibility.Feature
compareTo(Feature) - Method in class etomica.compatibility.NumericFeature
compareTo(int, Feature) - Method in class etomica.compatibility.NumericFeature
compareTo(Feature) - Method in class etomica.compatibility.StringFeature
compareTo(int, Feature) - Method in class etomica.compatibility.StringFeature
compareTo(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
compareTo(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
compareTo(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
compareTo(Graph) - Method in class etomica.graph.model.impl.GraphImpl
compareTo(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
compareTo(Node) - Method in class etomica.graph.model.impl.NodeImpl
compareTo(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd: Compares the value of this with another constant.
compareTo(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec: Compare algebraic value with oth.
compareTo(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Compare value against another Ifactor
compareTo(Rational) - Method in class etomica.veos.bigdecimal.Rational: Compares the value of this with another constant.
compareTo(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Compares the value of this with another constant.
compareTo(IntSet) - Method in class etomica.virial.IntSet
compareTo(MeterVirialExternalFieldSW.Near) - Method in class etomica.virial.MeterVirialExternalFieldSW.Near
completeCommand(Map<String, Token>, boolean, boolean, String, int) - Static method in class org.jmol.script.Token
COMPLETED - Static variable in class etomica.action.activity.Controller.ActionStatus
completedActions - Variable in class etomica.action.activity.ActivityGroupSeries
Complex - Class in etomica.math: handle complex variables and relevant operations from Internet
Complex(double, double) - Constructor for class etomica.math.Complex: Constructs the complex number z = u + i*v
component - Variable in class etomica.graphics.DeviceSlider: Object with property being modulated
component - Variable in class etomica.graphics.DeviceSpinner: Object with property being modulated
component - Variable in class etomica.models.co2.PNCO2GCPM
component - Variable in class etomica.models.co2.PNGCPM
component - Variable in class etomica.models.water.P2WaterSzalewicz
component(int, int) - Method in interface etomica.space.Tensor
component(int, int) - Method in class etomica.space1d.Tensor1D
component(int, int) - Method in class etomica.space2d.Tensor2D
component(int, int) - Method in class etomica.space3d.Tensor3D
component(int, int) - Method in class etomica.spaceNd.TensorND
ComponentEventControllerButton() - Constructor for class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
ComponentEventMyPanel() - Constructor for class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
componentHidden(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
componentHidden(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
componentMoved(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
componentMoved(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
componentResized(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
componentResized(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
componentShown(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
componentShown(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
ComponentSubst - Class in etomica.graph.operations: This class handles the substitution g = A where g is a Graph and A is a set of Graph.
ComponentSubst() - Constructor for class etomica.graph.operations.ComponentSubst
ComponentSubst.ComponentSubstParameters - Class in etomica.graph.operations
ComponentSubstParameters(Graph, Set<Graph>, MulFlexible.MulFlexibleParameters) - Constructor for class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
CompoundDimension - Class in etomica.units
CompoundDimension(Dimension[], double[]) - Constructor for class etomica.units.CompoundDimension
CompoundDimension(Dimension[], double[], String) - Constructor for class etomica.units.CompoundDimension
CompoundUnit - Class in etomica.units
CompoundUnit(Unit[], double[]) - Constructor for class etomica.units.CompoundUnit
CompoundUnit(Unit[], double[], String, String) - Constructor for class etomica.units.CompoundUnit
compressibility - Variable in class etomica.virial.HypernettedChain
compressibility - Variable in class etomica.virial.PercusYevick
compressibility - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
compressibility - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
compressibility - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
compressibility - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
compute() - Method in class etomica.veos.bigdecimal.Wigner3jGUI
computeA(int[], int[], double) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
computeA(int[], double[], double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
computeA(int[], int[], double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
computeA(int[], double[], double) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
computeAngle(Tuple3f, Tuple3f, Tuple3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
computeAngleABC(Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
computeAPartitions(int, int) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
computeB(double[], int, double, boolean) - Static method in class etomica.virial.B3ForSphericallySymmetricU
computeB(int, int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnIETP2Spherical
computeB(int, int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
computeB(double[], int, int, double, boolean) - Method in class etomica.virial.HypernettedChain
computeB(double[], int, int, double, boolean) - Method in class etomica.virial.PercusYevick
computeB(double[], int, int, double, boolean) - Method in class etomica.virial.PercusYevick1QC
computeB2QM(Potential2SoftSpherical, double) - Static method in class etomica.virial.B3ForSphericallySymmetricU
computeB3NonAdd(Potential2SoftSpherical, PotentialSoft, Space, double) - Static method in class etomica.virial.B3NonAddForSphericallySymmetricU
computeDstFiles(List) - Method in class etomica.graph.view.rasterizer.SVGConverter: Populates a vector with destination files names computed from the names of the files in the sources vector and the value of the dst property
computeHelicalAxis(String, int, Point3f, Point3f, Quaternion) - Static method in class org.jmol.util.Measure
computeImageParameters() - Method in class etomica.graphics.DisplayBox
computeImageParameters() - Method in class etomica.graphics.DisplayPolytope
computeImageParameters2(int, int) - Method in class etomica.graphics.DisplayBox
computeImageParameters2(int, int) - Method in class etomica.graphics.DisplayPolytope
computeOrigin(int, int, int) - Method in class etomica.graphics.DisplayPolytope
computeP - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
computeP - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
computePartitions(int, int) - Method in class etomica.virial.ClusterSinglyConnected
computePMA - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
computePMA - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
computeRMSD(double[]) - Method in class etomica.util.numerical.NonLinearCurveDiffFitting
computeRMSD(double[]) - Method in class etomica.util.numerical.NonLinearCurveFitting
computeScaledSysParams(double, double, double, double) - Static method in class etomica.potential.EwaldSummation
computeShiftOrigin(IAtom, IBoundary) - Method in class etomica.graphics.DisplayBoxCanvas1D
computeSources() - Method in class etomica.graph.view.rasterizer.SVGConverter: Populates a vector with the set of SVG files from the srcDir if it is not null and with the sources (files or URLs) if any.
computeTorsion(Tuple3f, Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
computeTranscodingHints() - Method in class etomica.graph.view.rasterizer.SVGConverter: Computes the set of transcoding hints to use for the operation
computeU - Variable in class etomica.mappedvirial.MappedU.LJMDParams
computeUMA - Variable in class etomica.mappedvirial.MappedU.LJMDParams
comWi - Variable in class etomica.models.water.PNWaterGCPM
comWj - Variable in class etomica.models.water.PNWaterGCPM
concatList(ScriptVariable, ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
concatTokens(String[], int, int) - Static method in class org.jmol.util.Parser
CondenseExchange - Class in etomica.virial.cluster: This operation replaces groups of points connected (internally) by e-exchange bonds with a single point.
CondenseExchange() - Constructor for class etomica.virial.cluster.CondenseExchange
CondenseExchange.CondenseExchangeParameters - Class in etomica.virial.cluster
CondenseExchangeParameters(char, char, char, char) - Constructor for class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
config - Variable in class etomica.interfacial.LJMC
config - Variable in class etomica.interfacial.LJMD
config - Variable in class etomica.modules.catalysis.Catalysis
config - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
config - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
config - Variable in class etomica.modules.dcvgcmd.DCVGCMD
config - Variable in class etomica.modules.droplet.Droplet
config - Variable in class etomica.modules.materialfracture.MaterialFracture
config - Variable in class etomica.modules.pistoncylinder.PistonCylinder
config - Variable in class etomica.modules.sam.Sam
configButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
configFile - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
configFile - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
configMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosis
configMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
configMonoLattice - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
configOrthoLattice - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
configuration - Variable in class etomica.action.SimulationRestart
Configuration - Interface in etomica.config: General class for assignment of molecules to positions in a box.
configuration - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
configuration - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
configuration - Variable in class etomica.modules.colloid.ColloidSim
configuration - Variable in class etomica.modules.mu.Mu
configuration - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
configuration - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
configuration - Static variable in class org.jmol.script.Token
ConfigurationAligned - Class in etomica.spin: Configuration used to align all atoms in a spin system, so all point in the same direction.
ConfigurationAligned() - Constructor for class etomica.spin.ConfigurationAligned
ConfigurationCatalysis - Class in etomica.modules.catalysis: Configuration for catalysis module.
ConfigurationCatalysis(ISimulation, ISpace, ISpecies, ISpecies, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.ConfigurationCatalysis
ConfigurationCatalysis.BasisOrthorhombicHexagonal3D - Class in etomica.modules.catalysis
ConfigurationCluster - Class in etomica.virial
ConfigurationCluster(ISpace) - Constructor for class etomica.virial.ConfigurationCluster
ConfigurationClusterAceticAcid - Class in etomica.virial
ConfigurationClusterAceticAcid(ISpace, IRandom, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
ConfigurationClusterAceticAcid(ISpace, IRandom, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
ConfigurationClusterAceticAcid(ISpace, IRandom, MayerFunction, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
ConfigurationClusterChain - Class in etomica.virial
ConfigurationClusterChain(ISpace) - Constructor for class etomica.virial.ConfigurationClusterChain
ConfigurationClusterChainFourSites - Class in etomica.virial
ConfigurationClusterChainFourSites(ISpace) - Constructor for class etomica.virial.ConfigurationClusterChainFourSites
ConfigurationClusterMove - Class in etomica.virial
ConfigurationClusterMove(ISpace, IRandom) - Constructor for class etomica.virial.ConfigurationClusterMove
ConfigurationClusterMove(ISpace, IRandom, double) - Constructor for class etomica.virial.ConfigurationClusterMove
ConfigurationClusterWertheimGCPM - Class in etomica.virial
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
ConfigurationClusterWertheimGCPM4Pt - Class in etomica.virial
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPM4Pt(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
ConfigurationClusterWertheimGCPMDirectSampling - Class in etomica.virial
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationClusterWertheimGCPMDirectSampling(ISpace, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
ConfigurationColloid - Class in etomica.modules.colloid
ConfigurationColloid(ISpace, ISpecies, ISpecies, IRandom) - Constructor for class etomica.modules.colloid.ConfigurationColloid
ConfigurationDroplet - Class in etomica.modules.droplet
ConfigurationDroplet(IRandom, ISpace) - Constructor for class etomica.modules.droplet.ConfigurationDroplet
ConfigurationFile - Class in etomica.config: reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationFile(String) - Constructor for class etomica.config.ConfigurationFile
ConfigurationFileBinary - Class in etomica.config: reads configuration coordinates from a binary file and assigns them to the leaf atoms in a box.
ConfigurationFileBinary(String) - Constructor for class etomica.config.ConfigurationFileBinary
ConfigurationFileTIP4P - Class in etomica.models.water: This reads from a configuration file containing only H, H and O.
ConfigurationFileTIP4P(String, ISpace, boolean) - Constructor for class etomica.models.water.ConfigurationFileTIP4P
ConfigurationFileXYZ - Class in etomica.zeolite
ConfigurationFileXYZ(String, ISpace) - Constructor for class etomica.zeolite.ConfigurationFileXYZ
ConfigurationLammps - Class in etomica.interfacial
ConfigurationLammps(ISpace, String, ISpecies, ISpecies, ISpecies) - Constructor for class etomica.interfacial.ConfigurationLammps
ConfigurationLattice - Class in etomica.config: Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLattice(SpaceLattice, ISpace) - Constructor for class etomica.config.ConfigurationLattice: Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationLattice(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.config.ConfigurationLattice: Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationLattice.MyLattice - Class in etomica.config: Used to store the state of a lattice.
ConfigurationLatticeFreeRadical - Class in etomica.modules.chainequilibrium: Configuration that puts atoms randomly on a lattice and groups pairs of initiator atoms together as though they are a single molecule.
ConfigurationLatticeFreeRadical(SpaceLattice, ISpace, IRandom) - Constructor for class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
ConfigurationLatticeRandom - Class in etomica.modules.chainequilibrium: Configuration that puts atoms randomly on a lattice.
ConfigurationLatticeRandom(SpaceLattice, ISpace, IRandom) - Constructor for class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
ConfigurationLatticeSimple - Class in etomica.config: Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLatticeSimple(SpaceLattice, ISpace) - Constructor for class etomica.config.ConfigurationLatticeSimple: Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationLatticeSimple(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.config.ConfigurationLatticeSimple: Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationLatticeTube - Class in etomica.modules.dcvgcmd: Creates a configuration using a CubicLattice to specify positions.
ConfigurationLatticeTube(BravaisLatticeCrystal, double, ISpace) - Constructor for class etomica.modules.dcvgcmd.ConfigurationLatticeTube
ConfigurationLatticeTube(BravaisLatticeCrystal, double, IndexIteratorSizable, ISpace) - Constructor for class etomica.modules.dcvgcmd.ConfigurationLatticeTube: Constructor for ConfigurationLatticeTube.
ConfigurationLatticeWithPlane - Class in etomica.config: Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationLatticeWithPlane(SpaceLattice, Plane, ISpace) - Constructor for class etomica.config.ConfigurationLatticeWithPlane: Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationMembrane - Class in etomica.modules.rosmosis
ConfigurationMembrane(ISimulation, ISpace) - Constructor for class etomica.modules.rosmosis.ConfigurationMembrane
ConfigurationMembraneWater - Class in etomica.modules.rosmosis
ConfigurationMembraneWater(ISimulation, Space) - Constructor for class etomica.modules.rosmosis.ConfigurationMembraneWater
ConfigurationMonoclinicLattice - Class in etomica.paracetamol: Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationMonoclinicLattice(SpaceLattice, ISpace) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice: Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationMonoclinicLattice(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice: Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationMonoclinicLattice.MyLattice - Class in etomica.paracetamol: Used to store the state of a lattice.
ConfigurationOrientedFile - Class in etomica.config: ConfigurationFile subclass capable of handling oriented atoms.
ConfigurationOrientedFile(String, ISpace) - Constructor for class etomica.config.ConfigurationOrientedFile
ConfigurationOrthorhombicLattice - Class in etomica.paracetamol: Constructs configuration that has the molecules placed on the sites of a lattice.
ConfigurationOrthorhombicLattice(SpaceLattice, ISpace) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice: Constructs class using instance of IndexIteratorRectangular as the default index iterator.
ConfigurationOrthorhombicLattice(SpaceLattice, IndexIteratorSizable, ISpace) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice: Construct class that will place atoms on sites of the given lattice, proceeding in the order resulting from iteration through the given index iterator.
ConfigurationOrthorhombicLattice.MyLattice - Class in etomica.paracetamol: Used to store the state of a lattice.
ConfigurationOverlapException - Exception in etomica.exception: Exception thrown when an overlap is detected in the configuration of a box, subject to the status of an ignoreOverlap flag.
ConfigurationOverlapException(IBox) - Constructor for exception etomica.exception.ConfigurationOverlapException: Constructor for ConfigurationOverlapException
ConfigurationReplicate - Class in etomica.config
ConfigurationReplicate() - Constructor for class etomica.config.ConfigurationReplicate
ConfigurationSAM - Class in etomica.modules.sam
ConfigurationSAM(ISimulation, ISpace, ISpecies, ISpecies, PotentialMasterList) - Constructor for class etomica.modules.sam.ConfigurationSAM
ConfigurationWater108 - Class in etomica.rotation: reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater108() - Constructor for class etomica.rotation.ConfigurationWater108
ConfigurationWater108TIP4P - Class in etomica.rotation: reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater108TIP4P() - Constructor for class etomica.rotation.ConfigurationWater108TIP4P
ConfigurationWater256 - Class in etomica.rotation: reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater256() - Constructor for class etomica.rotation.ConfigurationWater256
ConfigurationWater3 - Class in etomica.rotation: reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater3() - Constructor for class etomica.rotation.ConfigurationWater3
ConfigurationWater3_3P - Class in etomica.rotation: reads configuration coordinates from a file and assigns them to the leaf atoms in a box
ConfigurationWater3_3P() - Constructor for class etomica.rotation.ConfigurationWater3_3P
ConfigurationZero - Class in etomica.modules.entropylottery: Configuration that simply puts all the Atoms at 0, or -0.5 if the box size is even (which makes the entropy lottery binning happy).
ConfigurationZero(ISpace) - Constructor for class etomica.modules.entropylottery.ConfigurationZero
ConfigurationZincblende - Class in etomica.config: Sets the configuration to the zincblende structure, which consists of two fcc lattices, with one shifted in each direction by one-quarter of the lattice constant.
ConfigurationZincblende(double, ISpace) - Constructor for class etomica.config.ConfigurationZincblende
confluentHypergeometric1F1(double, double, double) - Static method in class etomica.math.SpecialFunctions: The confluent hypergeometric function, usually given the symbol 1F1.
confName - Variable in class etomica.action.WriteConfiguration
confName - Variable in class etomica.config.ConfigurationFile
confName - Variable in class etomica.config.ConfigurationFileBinary
conformation - Variable in class etomica.chem.models.ModelChain
conformation - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
conformation - Variable in class etomica.modules.rheology.SimulationRheology
conformation - Variable in class etomica.modules.sam.ConfigurationSAM
conformation - Variable in class etomica.species.Species
conformation - Variable in class etomica.virial.SpeciesFactoryWater4P
Conformation7SiteRigidSF6 - Class in etomica.virial: Conformation of SF6 7 LJ sites, rigid, no charge Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
Conformation7SiteRigidSF6(ISpace) - Constructor for class etomica.virial.Conformation7SiteRigidSF6
ConformationAceticAcid - Class in etomica.models.OPLS: Conformation for acetic acid
ConformationAceticAcid(ISpace) - Constructor for class etomica.models.OPLS.ConformationAceticAcid
ConformationAlkaneEH - Class in etomica.AlkaneEH: Conformation for normal alkanes, explicit hydrogen Siepmann, TraPPE-EH
ConformationAlkaneEH(ISpace, SpeciesAlkaneEH) - Constructor for class etomica.AlkaneEH.ConformationAlkaneEH
ConformationAlkaneEH - Class in etomica.virial: Conformation for normal alkanes, explicit hydrogen Siepmann, TraPPE-EH
ConformationAlkaneEH(ISpace, SpeciesAlkaneEH) - Constructor for class etomica.virial.ConformationAlkaneEH
ConformationAnthracene3site - Class in etomica.virial: Conformation for Anthracene Reference paper: Iwai 3 site linear, group H to the two side benzene rings
ConformationAnthracene3site(ISpace) - Constructor for class etomica.virial.ConformationAnthracene3site
ConformationAnthraceneTraPPE - Class in etomica.virial: Conformation for Anthracene Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al modified from naphthalene conformation
ConformationAnthraceneTraPPE(ISpace) - Constructor for class etomica.virial.ConformationAnthraceneTraPPE
ConformationChain - Class in etomica.config: General class for a collection of linearly linked atoms.
ConformationChain(ISpace) - Constructor for class etomica.config.ConformationChain
ConformationChain2D - Class in etomica.config
ConformationChain2D(ISpace, IVector[]) - Constructor for class etomica.config.ConformationChain2D
ConformationChain3D - Class in etomica.config
ConformationChain3D(ISpace, IVector[]) - Constructor for class etomica.config.ConformationChain3D
ConformationChainLinear - Class in etomica.config: Places atoms in a straight line.
ConformationChainLinear(ISpace) - Constructor for class etomica.config.ConformationChainLinear
ConformationChainLinear(ISpace, double) - Constructor for class etomica.config.ConformationChainLinear
ConformationChainLinear(ISpace, double, double[]) - Constructor for class etomica.config.ConformationChainLinear
ConformationChainZigZag - Class in etomica.config: Takes two vectors, and returns them in repeating order to form a zig-zag chain molecule.
ConformationChainZigZag(ISpace) - Constructor for class etomica.config.ConformationChainZigZag
ConformationChainZigZag(ISpace, IVector, IVector) - Constructor for class etomica.config.ConformationChainZigZag
ConformationChainZigZag2 - Class in etomica.config
ConformationChainZigZag2(ISpace) - Constructor for class etomica.config.ConformationChainZigZag2
ConformationChainZigZag2(ISpace, IVector, IVector) - Constructor for class etomica.config.ConformationChainZigZag2
ConformationCO2 - Class in etomica.virial: Conformation for CO2 Reference paper: Partial molar ~~, Stubbs Darke-Wilhelm, Siepmann, JCP
ConformationCO2(ISpace) - Constructor for class etomica.virial.ConformationCO2
ConformationEthanol - Class in etomica.models.rowley: Conformation for ethanol (positioned in standard orientation) as published in Rowley et al (2006) K.R.
ConformationEthanol(ISpace, boolean) - Constructor for class etomica.models.rowley.ConformationEthanol
ConformationGeneric - Class in etomica.config
ConformationGeneric(IVector[]) - Constructor for class etomica.config.ConformationGeneric
ConformationHexane - Class in etomica.models.hexane: Defines the vectors used to create a hexane molecule according to Dr.
ConformationHexane(ISpace) - Constructor for class etomica.models.hexane.ConformationHexane
ConformationHSDimer - Class in etomica.normalmode: Conformation for HS Dimer
ConformationHSDimer(ISpace, double) - Constructor for class etomica.normalmode.ConformationHSDimer
ConformationLinear - Class in etomica.config: Places atoms in a straight line.
ConformationLinear(ISpace) - Constructor for class etomica.config.ConformationLinear
ConformationLinear(ISpace, double) - Constructor for class etomica.config.ConformationLinear
ConformationLinear(ISpace, double, double[]) - Constructor for class etomica.config.ConformationLinear
ConformationMethane - Class in etomica.AlkaneEH: Conformation for TraPPE-Explicit hydrogen methane C site and H site, NOTE the H is located in the middle of C-H bond
ConformationMethane(ISpace) - Constructor for class etomica.AlkaneEH.ConformationMethane
ConformationMethane - Class in etomica.virial: Conformation for TraPPE-Explicit hydrogen methane C site and H site, NOTE the H is located in the middle of C-H bond
ConformationMethane(ISpace) - Constructor for class etomica.virial.ConformationMethane
ConformationMethanol - Class in etomica.models.rowley: Conformation for methanol in standard orientation as published in Rowley et al (2006) OpenOffice Spreadsheet file, Methanol coordinates, used to calculate coordinates from bond lengths and angles: K.R.
ConformationMethanol(ISpace, boolean) - Constructor for class etomica.models.rowley.ConformationMethanol
ConformationMethanol - Class in etomica.models.traPPE: Conformation for TraPPE model of methanol: http://www.chem.umn.edu/groups/siepmann/trappe/molname.php# CH3 group of methanol is united into a single site K.R.
ConformationMethanol(ISpace) - Constructor for class etomica.models.traPPE.ConformationMethanol
ConformationNaphthaleneTraPPE - Class in etomica.virial: Conformation for Naphthalene Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
ConformationNaphthaleneTraPPE(ISpace) - Constructor for class etomica.virial.ConformationNaphthaleneTraPPE
ConformationNitrogen - Class in etomica.models.nitrogen: Conformation for Nitrogen Reference paper: Etters RD.
ConformationNitrogen(ISpace) - Constructor for class etomica.models.nitrogen.ConformationNitrogen
ConformationNitrogenShellModel - Class in etomica.models.nitrogen: Conformation for Nitrogen (Shell Model) Reference: Fabianski R.
ConformationNitrogenShellModel(ISpace) - Constructor for class etomica.models.nitrogen.ConformationNitrogenShellModel
ConformationParacetamol - Class in etomica.paracetamol
ConformationParacetamol(ISpace) - Constructor for class etomica.paracetamol.ConformationParacetamol
ConformationParacetamolMonoclinic - Class in etomica.paracetamol
ConformationParacetamolMonoclinic(ISpace) - Constructor for class etomica.paracetamol.ConformationParacetamolMonoclinic
ConformationParacetamolOrthorhombic - Class in etomica.paracetamol
ConformationParacetamolOrthorhombic(ISpace) - Constructor for class etomica.paracetamol.ConformationParacetamolOrthorhombic
ConformationPh3site - Class in etomica.virial: Conformation for Phenanthrene Reference paper: Iwai 3 site group H to the two side benzene rings , eihter 464 or 545 model modified from ConformationAnthracene
ConformationPh3site(ISpace) - Constructor for class etomica.virial.ConformationPh3site
ConformationPhenanthreneTraPPE - Class in etomica.virial: Conformation for Phenanthrene Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al modified from naphthalene kept the axis and coorinated unchanged
ConformationPhenanthreneTraPPE(ISpace) - Constructor for class etomica.virial.ConformationPhenanthreneTraPPE
ConformationPolymer - Class in etomica.modules.rheology: Places polymer in a blob near the origin.
ConformationPolymer(ISpace, IRandom) - Constructor for class etomica.modules.rheology.ConformationPolymer
ConformationTube - Class in etomica.modules.dcvgcmd
ConformationTube(ISpace, int) - Constructor for class etomica.modules.dcvgcmd.ConformationTube
ConformationWater - Class in etomica.config
ConformationWater(ISpace) - Constructor for class etomica.config.ConformationWater
ConformationWater3P - Class in etomica.models.water: Conformation for 3-point water molecule.
ConformationWater3P(ISpace) - Constructor for class etomica.models.water.ConformationWater3P
ConformationWaterGCPM - Class in etomica.models.water
ConformationWaterGCPM(ISpace) - Constructor for class etomica.models.water.ConformationWaterGCPM
ConformationWaterGCPMCOM - Class in etomica.models.water: Conformation for 4-point water molecule (plus 1 site at the COM).
ConformationWaterGCPMCOM(ISpace) - Constructor for class etomica.models.water.ConformationWaterGCPMCOM
ConformationWaterTIP4P - Class in etomica.models.water: Conformation for 4-point water molecule.
ConformationWaterTIP4P(ISpace) - Constructor for class etomica.models.water.ConformationWaterTIP4P
conjugate() - Method in class etomica.math.Complex: Complex conjugate of this Complex number (the conjugate of x+i*y is x-i*y).
conjugate() - Method in class etomica.math.Quaternion: Returns the complex conjugate of the Quaternion q.
ConjugateGradients - Class in etomica.conjugategradient
ConjugateGradients(Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.ConjugateGradients
ConjugateGradientsAlgorithm() - Method in class etomica.conjugategradient.ConjugateGradients: Conjugate Gradients solution for Ax = b
connect - Static variable in class org.jmol.script.Token
connected - Static variable in class org.jmol.script.Token
ConnectedToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ConnectedToggler
Console - Interface in etomica.graph.engine
ConsoleContainer - Interface in etomica.graph.engine
ConsoleReader - Interface in etomica.graph.engine
ConsoleUI - Class in etomica.graph.engine
ConsoleUI() - Constructor for class etomica.graph.engine.ConsoleUI
ConsoleWindow(ConsoleUI) - Constructor for class etomica.graph.engine.Launcher.ConsoleWindow
ConsoleWindowRunnable(Launcher.ConsoleWindow) - Constructor for class etomica.graph.engine.Launcher.ConsoleWindowRunnable
Constant() - Constructor for class etomica.util.Function.Constant
Constant(double) - Constructor for class etomica.util.Function.Constant
Constants - Class in etomica.util: Collection of assorted physical constants.
Constants.Alignment - Class in etomica.util: Enumerated type for specifying HORIZONTAL/VERTICAL alignment.
Constants.CompassDirection - Class in etomica.util: Enumerated type for the compass directions NORTH, SOUTH, EAST, WEST.
Constants.Direction - Class in etomica.util: Enumerated type for the directions TOP, BOTTOM, LEFT, RIGHT, FRONT, BACK.
constMu - Variable in class etomica.modules.ensembles.LJMCGraphic
constrainScriptOrigin - Variable in class etomica.graph.view.rasterizer.SVGConverter: Controls whether scripts can only have the same origin as the document which references them.
constraint - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
constraint - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
constraint - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
constraint - Variable in class etomica.normalmode.P1ConstraintNbr
constraintAngle - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
constraintAngle - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
constraintAngle - Variable in class etomica.models.nitrogen.MeterDirectInitPert
constraintAngle - Variable in class etomica.models.nitrogen.PRotConstraint
constraintAngle - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterBoltzmannHTTP: Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterDDP: Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterDP: Returns true if all atoms in the given box satisfy p1's constraint
constraintEnergy(IBox) - Method in class etomica.normalmode.MeterTargetTP: Returns true if all atoms in the given box satisfy p1's constraint
constraintMap - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
constraintMap - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
constraintPotential - Variable in class etomica.normalmode.MCMoveAtomCoupled
constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
CONSTRUCTOR_COLORED - Static variable in interface etomica.graph.engine.Parser
CONSTRUCTOR_ISOCOLORED - Static variable in interface etomica.graph.engine.Parser
CONSTRUCTOR_ISOMONO - Static variable in interface etomica.graph.engine.Parser
CONSTRUCTOR_MONO - Static variable in interface etomica.graph.engine.Parser
ConstructorColoredImpl - Class in etomica.graph.engine.impl
ConstructorColoredImpl(Map<Character, Byte>, Map<Character, Byte>, boolean) - Constructor for class etomica.graph.engine.impl.ConstructorColoredImpl
ConstructorImpl - Class in etomica.graph.engine.impl
ConstructorImpl() - Constructor for class etomica.graph.engine.impl.ConstructorImpl
ConstructorMonoImpl - Class in etomica.graph.engine.impl
ConstructorMonoImpl(byte, byte, boolean) - Constructor for class etomica.graph.engine.impl.ConstructorMonoImpl
cont - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
contact - Static variable in class org.jmol.script.Token
contains(IAtom) - Method in class etomica.atom.AtomArrayList: Returns true if the given atom is in the list, false otherwise
CONTAINS - Static variable in class etomica.compatibility.Feature
contains(Object) - Method in class etomica.graph.model.GraphList
contains(IVector) - Method in class etomica.math.geometry.Cube: Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Cuboid: Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Hypersphere: Returns true if the given point lies on or in the sphere.
contains(IVector) - Method in class etomica.math.geometry.LineSegment: Returns true if the given vector lies between the ends of the segment, on the line joining them.
contains(IVector) - Method in class etomica.math.geometry.Parallelepiped: Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Parallelogram: Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Point: Returns true if this point is at exactly the same location as the point defined by the given vector.
contains(IVector) - Method in class etomica.math.geometry.PolygonGeneral: Returns true if the given point lies inside or on an edge of the polygon
contains(IVector) - Method in class etomica.math.geometry.PolyhedronGeneral: Returns true if the given point lies inside or on an edge of the polyhedron
contains(IVector) - Method in class etomica.math.geometry.Polytope: Returns true if the given vector lies inside the polytope, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.Rectangle: Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in interface etomica.math.geometry.Shape: Returns true if the point described by the vector lies in or on the enclosed region.
contains(IVector) - Method in class etomica.math.geometry.Square: Returns true if the given vector lies inside (or on the surface of) this cell, false otherwise.
contains(IVector) - Method in class etomica.math.geometry.TruncatedOctahedron
contains(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
contains(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup: Indicates if a given potential is a sub-potential of this group.
contains(double) - Method in class etomica.util.DoubleRange: Indicates if a value falls within the range of this instance.
contains(int) - Method in class etomica.util.IntegerRange: Indicates if a value falls within the range of this instance.
contains(Object) - Method in class etomica.util.ObjectArrayList: Returns true if this list contains the specified element.
contains(BigInteger) - Method in class etomica.veos.bigdecimal.Prime: Test if a number is a prime.
containsAll(Collection<?>) - Method in class etomica.graph.model.GraphList
continuous - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
continuous - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
contourlines - Static variable in class org.jmol.script.Token
controlGraphic() - Method in class etomica.graphics.DevicePlotPoints: Returns the top level panel that the points table and (if parameters are vertically-oriented) function parameter slider components sit on.
Controller - Class in etomica.action.activity: Organizer and executor of actions performed by the simulation.
Controller() - Constructor for class etomica.action.activity.Controller
controller - Variable in class etomica.action.activity.ControllerEvent
controller - Variable in class etomica.action.ControllerActionAdapter
controller - Variable in class etomica.AlkaneEH.CH4NVT
controller - Variable in class etomica.AlkaneEH.DHS_NVT
controller - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
controller - Variable in class etomica.densityofstate.DensityOfState
controller - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
controller - Variable in class etomica.dielectric.DHS_NVT
controller - Variable in class etomica.dielectric.DLJ_NVT_1site
controller - Variable in class etomica.dielectric.TIP4P_NVT
controller - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
controller - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
controller - Variable in class etomica.graph.view.rasterizer.SVGConverter: Controls some aspects of the converter's operation, such as whether or not it should proceed in some error situations.
controller - Variable in class etomica.graphics.Device
controller - Variable in class etomica.graphics.DisplayBox
controller - Variable in class etomica.graphics.DisplayCanvas
controller - Variable in class etomica.graphics.SimulationGraphic
controller - Variable in class etomica.meam.EFSTungsten
controller - Variable in class etomica.meam.MEAM_3DMDwithGB
controller - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
controller - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
controller - Variable in class etomica.meam.MEAM_MC
controller - Variable in class etomica.meam.MEAMMd3D
controller - Variable in class etomica.normalmode.SimOverlapModule
controller - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
controller - Variable in class etomica.simulation.prototypes.HsMc2d
controller - Variable in class etomica.simulation.prototypes.LjMd2D
controller - Variable in class etomica.simulation.prototypes.LjMd3D
controller - Variable in class etomica.simulation.prototypes.SoftSphere3d
controller - Variable in class etomica.simulation.prototypes.SwMd2D
controller - Variable in class etomica.simulation.prototypes.SWMD3D
controller - Variable in class etomica.tests.TestLJMC3D
controller - Variable in class etomica.thermointegration.LjMc3D
controller - Variable in class etomica.threaded.atom.LJMD3DThreaded
controller - Variable in class etomica.threaded.domain.LJMD3DThreaded
controller - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
controller - Variable in class etomica.yukawa.TestHC2YukawaMC3D
controller - Variable in class etomica.yukawa.TestYukawaMC3D
Controller.ActionStatus - Class in etomica.action.activity: Enumerated type describing the status of an action.
Controller.UrgentWaitObject - Class in etomica.action.activity
Controller.WaitObject - Class in etomica.action.activity
controller1 - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
controller1 - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
controller1 - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
ControllerAction - Interface in etomica.action: Elementary action performed on a controller.
ControllerActionAdapter - Class in etomica.action: Convenience class used to define a ControllerAction.
ControllerActionAdapter() - Constructor for class etomica.action.ControllerActionAdapter
ControllerAlertMsgBox - Class in etomica.virial.GUI.controllers
ControllerAlertMsgBox(String, ModelSpeciesSelection) - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBox
ControllerAlertMsgBox.CloseWindowButtonListener - Class in etomica.virial.GUI.controllers
ControllerAlertMsgBoxSpeciesRemoval - Class in etomica.virial.GUI.controllers
ControllerAlertMsgBoxSpeciesRemoval(String, ModelSpeciesSelection, int) - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval
ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener - Class in etomica.virial.GUI.controllers
ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener - Class in etomica.virial.GUI.controllers
ControllerAlkaneLengthSelection - Class in etomica.virial.GUI.controllers
ControllerAlkaneLengthSelection(ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
ControllerEvent - Class in etomica.action.activity
ControllerEvent(IController, ControllerEvent.Type) - Constructor for class etomica.action.activity.ControllerEvent
ControllerEvent(IController, ControllerEvent.Type, IAction) - Constructor for class etomica.action.activity.ControllerEvent
ControllerEvent.Type - Class in etomica.action.activity
ControllerEventManager - Class in etomica.action.activity
ControllerEventManager() - Constructor for class etomica.action.activity.ControllerEventManager
ControllerSimEnvironmentSelection - Class in etomica.virial.GUI.controllers
ControllerSimEnvironmentSelection(ModelSimulationEnvironment) - Constructor for class etomica.virial.GUI.controllers.ControllerSimEnvironmentSelection
controllerSpeciesSelection - Variable in class etomica.virial.GUI.controllers.AppControllerMixtureBuilder
ControllerSpeciesSelection - Class in etomica.virial.GUI.controllers
ControllerToggle - Class in etomica.action: Switches controller between paused and unpaused conditions, or starts it if not yet active.
ControllerToggle() - Constructor for class etomica.action.ControllerToggle
controlPanel - Variable in class etomica.graphics.SimulationPanel
contructFullMatrix(CoordinateDefinition, String) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
contructFullMatrix(CoordinateDefinition, String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
Conv - Class in etomica.graph.operations
Conv() - Constructor for class etomica.graph.operations.Conv
Converter(String) - Static method in class etomica.zeolite.Zeolite
Converter(String) - Static method in class etomica.zeolite.ZeoliteSimulation
convertPointFromScreen(Object, Point3f) - Method in interface org.jmol.api.ApiPlatform
convertPointFromScreen(Object, Point3f) - Method in class org.jmol.awt.Platform
convolution(ClusterDiagram, ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations: Returns a new cluster that is a convolution of the given cluster, which is obtained by joining a root point from each diagram and turning it into a field point.
convolution(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Returns an array of clusters formed from taking the convolution of each of the diagrams of the first set with each of the diagrams of the second set.
ConvParameters - Class in etomica.graph.operations
ConvParameters(byte, Mul.MulParameters) - Constructor for class etomica.graph.operations.ConvParameters
coord - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
coord2 - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
coord3 - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
coordDef - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
coordDef - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
coordDef - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
CoordinateConverter - Class in etomica.math.geometry.coordinate
CoordinateConverter() - Constructor for class etomica.math.geometry.coordinate.CoordinateConverter
coordinateDef - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
coordinateDef - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
coordinateDef - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
coordinateDef - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
coordinateDef - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
coordinateDef - Variable in class etomica.models.nitrogen.MeterDirectInitPert
coordinateDef - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
coordinateDef - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
coordinateDef - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
coordinateDef - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
coordinateDef - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
coordinateDef - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
coordinateDef - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
coordinateDef - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
coordinateDefinition - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
coordinateDefinition - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
coordinateDefinition - Variable in class etomica.meam.EFSTungsten
coordinateDefinition - Variable in class etomica.meam.PotentialFeEAM_LS
coordinateDefinition - Variable in class etomica.models.hexane.SimHarmonicHexane
coordinateDefinition - Variable in class etomica.models.hexane.TestHexane
coordinateDefinition - Variable in class etomica.models.hexane.TestHexaneFileConfig
coordinateDefinition - Variable in class etomica.models.hexane.TestHexaneHarmonic
coordinateDefinition - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
coordinateDefinition - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
coordinateDefinition - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
coordinateDefinition - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
coordinateDefinition - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterNormalizedCoord
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterNormalizedCoordBeta
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterOrientationDistribution
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterOrientationOrderParameter
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterRotationDistributionGroup
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
coordinateDefinition - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
coordinateDefinition - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
coordinateDefinition - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
coordinateDefinition - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
coordinateDefinition - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
coordinateDefinition - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
coordinateDefinition - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimWidomMode
coordinateDefinition - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
coordinateDefinition - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
coordinateDefinition - Variable in class etomica.normalmode.CalcJacobian
CoordinateDefinition - Class in etomica.normalmode: An abstract class that defines the real-space generalized coordinates that are summed (over molecules) to form collective coordinates (from which normal coordinates are determined).
CoordinateDefinition(IBox, int, Primitive, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinition
CoordinateDefinition(IBox, int, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinition
coordinateDefinition - Variable in class etomica.normalmode.HessianDB
coordinateDefinition - Variable in class etomica.normalmode.HSDimerNPT
coordinateDefinition - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
coordinateDefinition - Variable in class etomica.normalmode.HSNPT
coordinateDefinition - Variable in class etomica.normalmode.HTTPSoftSphereSim
coordinateDefinition - Variable in class etomica.normalmode.IntegratorHarmonic
coordinateDefinition - Variable in class etomica.normalmode.LJVacancyMin
coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomSuperBox
coordinateDefinition - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
coordinateDefinition - Variable in class etomica.normalmode.MCMoveHarmonic
coordinateDefinition - Variable in class etomica.normalmode.MCMoveHarmonicStep
coordinateDefinition - Variable in class etomica.normalmode.MCMovePhaseAngle
coordinateDefinition - Variable in class etomica.normalmode.MCMoveSingleMode
coordinateDefinition - Variable in class etomica.normalmode.MCMoveVolumeSolid
coordinateDefinition - Variable in class etomica.normalmode.MCMoveWV
coordinateDefinition - Variable in class etomica.normalmode.MeterAtomicDisplacement
coordinateDefinition - Variable in class etomica.normalmode.MeterBoltzmannHTTP
coordinateDefinition - Variable in class etomica.normalmode.MeterDADB
coordinateDefinition - Variable in class etomica.normalmode.MeterDDP
coordinateDefinition - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
coordinateDefinition - Variable in class etomica.normalmode.MeterDisplacementRMS
coordinateDefinition - Variable in class etomica.normalmode.MeterDP
coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicCoordinate
coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicEnergy
coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
coordinateDefinition - Variable in class etomica.normalmode.MeterJacobian
coordinateDefinition - Variable in class etomica.normalmode.MeterNormalMode
coordinateDefinition - Variable in class etomica.normalmode.MeterSolidMirror
coordinateDefinition - Variable in class etomica.normalmode.MeterSolidProps
coordinateDefinition - Variable in class etomica.normalmode.MeterSolidPropsLJ
coordinateDefinition - Variable in class etomica.normalmode.MeterTargetTP
coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
coordinateDefinition - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
coordinateDefinition - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
coordinateDefinition - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationEFSSP
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationLJSP
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
coordinateDefinition - Variable in class etomica.normalmode.SimBennet
coordinateDefinition - Variable in class etomica.normalmode.SimCalcJ
coordinateDefinition - Variable in class etomica.normalmode.SimCalcS
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSLJ
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSMorse
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
coordinateDefinition - Variable in class etomica.normalmode.SimHarmonic
coordinateDefinition - Variable in class etomica.normalmode.SimHarmonicUmbrella
coordinateDefinition - Variable in class etomica.normalmode.SimLJHTTISuper
coordinateDefinition - Variable in class etomica.normalmode.SimLJHTTISuperHCP
coordinateDefinition - Variable in class etomica.normalmode.SimModesJ
coordinateDefinition - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
coordinateDefinition - Variable in class etomica.normalmode.SimTarget
coordinateDefinition - Variable in class etomica.normalmode.SimTargetUmbrella
coordinateDefinition - Variable in class etomica.normalmode.SimUmbrella
coordinateDefinition - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
coordinateDefinition - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
coordinateDefinition - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
coordinateDefinition - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
coordinateDefinition - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
CoordinateDefinition.BasisCell - Class in etomica.normalmode
CoordinateDefinition.SiteSource - Class in etomica.normalmode
CoordinateDefinitionHexane - Class in etomica.models.hexane: Implementation of CoordinateDefinitionMolecule that handles hexane.
CoordinateDefinitionHexane(ISimulation, IBox, Primitive, SpeciesHexane, ISpace) - Constructor for class etomica.models.hexane.CoordinateDefinitionHexane
CoordinateDefinitionHSDimer - Class in etomica.normalmode: CoordinateDefinition implementation for HS Dimer.
CoordinateDefinitionHSDimer(ISimulation, IBox, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionHSDimer
CoordinateDefinitionHSDimer.IntegerFunction - Interface in etomica.normalmode
CoordinateDefinitionLeaf - Class in etomica.normalmode: CoordinateDefinition implementation for monatomic molecules that are simply leaf atoms.
CoordinateDefinitionLeaf(IBox, Primitive, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionLeaf
CoordinateDefinitionLeaf(IBox, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionLeaf
CoordinateDefinitionLeafSuperBox - Class in etomica.normalmode
CoordinateDefinitionLeafSuperBox(IBox, Primitive, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionLeafSuperBox
CoordinateDefinitionMolecule - Class in etomica.normalmode: CoordinateDefinition implementation for molecules.
CoordinateDefinitionMolecule(ISimulation, IBox, Primitive, int, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule
CoordinateDefinitionMolecule(ISimulation, IBox, Primitive, int, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule
CoordinateDefinitionMolecule.MoleculeSiteSource - Class in etomica.normalmode
CoordinateDefinitionMoleculeVolumeFluctuation - Class in etomica.normalmode: CoordinateDefinition implementation for molecules.
CoordinateDefinitionMoleculeVolumeFluctuation(ISimulation, IBox, Primitive, int, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
CoordinateDefinitionMoleculeVolumeFluctuation(ISimulation, IBox, Primitive, int, Basis, ISpace) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource - Class in etomica.normalmode
CoordinateDefinitionNitrogen - Class in etomica.models.nitrogen: CoordinateDefinition implementation for nitrogen molecule.
CoordinateDefinitionNitrogen(ISimulation, IBox, Primitive, Basis, ISpace) - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogen
CoordinateDefinitionNitrogen(ISimulation, IBox, Primitive, Basis, ISpace, int) - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogen
CoordinateDefinitionNitrogen.OrientationAgentSource - Class in etomica.models.nitrogen
CoordinateDefinitionNitrogenSuperBox - Class in etomica.models.nitrogen: CoordinateDefinition implementation for nitrogen molecule.
CoordinateDefinitionNitrogenSuperBox(ISimulation, IBox, Primitive, Basis, ISpace) - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource - Class in etomica.models.nitrogen
CoordinateDefinitionParacetamol - Class in etomica.paracetamol: CoordinateDefinition implementation for paracetamol molecule.
CoordinateDefinitionParacetamol(ISimulation, IBox, Primitive, Basis, ISpace) - Constructor for class etomica.paracetamol.CoordinateDefinitionParacetamol
CoordinateDefinitionParacetamol.OrientationAgentSource - Class in etomica.paracetamol
coordinateDefTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
coordinateDim - Variable in class etomica.normalmode.CalcJacobian
coordinateDim - Variable in class etomica.normalmode.CoordinateDefinition
CoordinatePairLeafSet - Class in etomica.virial
CoordinatePairLeafSet(IAtomList, ISpace) - Constructor for class etomica.virial.CoordinatePairLeafSet: Constructor for CoordinatePairLeafSet.
CoordinatePairMoleculeSet - Class in etomica.virial
CoordinatePairMoleculeSet(IMoleculeList, ISpace) - Constructor for class etomica.virial.CoordinatePairMoleculeSet: Constructor for CoordinatePairLeafSet.
CoordinatePairSet - Interface in etomica.virial
coordinteDefinition - Variable in class etomica.normalmode.MeterSolidDA
coordinteDefinition - Variable in class etomica.normalmode.MeterSolidDACut
coords - Variable in class etomica.config.ConformationGeneric
Copper - Class in etomica.chem.elements: Class for the Copper element.
Copper(String) - Constructor for class etomica.chem.elements.Copper
Copper(String, double) - Constructor for class etomica.chem.elements.Copper
copy() - Method in interface etomica.graph.isomorphism.SearchState
copy(SearchState) - Method in interface etomica.graph.isomorphism.SearchState
copy() - Method in class etomica.graph.isomorphism.UllmanSearchState
copy(SearchState) - Method in class etomica.graph.isomorphism.UllmanSearchState
copy() - Method in class etomica.graph.isomorphism.VF2SearchState
copy(SearchState) - Method in class etomica.graph.isomorphism.VF2SearchState
copy() - Method in class etomica.graph.isomorphism.VFSearchState
copy(SearchState) - Method in class etomica.graph.isomorphism.VFSearchState
copy() - Method in interface etomica.graph.model.Bitmap: Creates an instance-compatible copy of this bitmap.
copy() - Method in interface etomica.graph.model.Coefficient
copy() - Method in interface etomica.graph.model.Edge
copy() - Method in interface etomica.graph.model.Graph
copy() - Method in class etomica.graph.model.impl.AbstractBitmap
copy() - Method in class etomica.graph.model.impl.CoefficientImpl
copy() - Method in class etomica.graph.model.impl.EdgeImpl
copy() - Method in class etomica.graph.model.impl.GraphImpl
copy() - Method in class etomica.graph.model.impl.NodeImpl
copy() - Method in interface etomica.graph.model.Node
copy() - Method in class etomica.lattice.crystal.Primitive: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveBcc: Returns a new PrimitiveCubic with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveCubic: Returns a new PrimitiveCubic with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveFcc: Returns a new PrimitiveCubic with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveGeneral
copy() - Method in class etomica.lattice.crystal.PrimitiveHexagonal: Returns a new PrimitiveHexagonal with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D: Returns a new PrimitiveHexagonal with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveTetragonal: Returns a new PrimitiveTetragonal with the same size as this one.
copy() - Method in class etomica.lattice.crystal.PrimitiveTriclinic: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.lattice.crystal.PrimitiveTrigonal: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.models.hexane.PrimitiveHexane: Returns a new, identical instance of this primitive.
copy() - Method in class etomica.virial.IntSet
copy(BitSet) - Static method in class org.jmol.util.BitSetUtil
copy2(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
copyColixTranslucency(short, short) - Static method in class org.jmol.util.Colix
copyFrom(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
copyFrom(String) - Method in class etomica.graph.model.impl.AbstractBitmap
copyFrom(byte[]) - Method in class etomica.graph.model.impl.AbstractBitmap
copyFrom(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1).
copyFrom(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
copyHighest(int) - Method in interface etomica.graph.model.Bitmap: Creates an instance-compatible copy of highest numBits bits of this bitmap.
copyHighest(int) - Method in class etomica.graph.model.impl.AbstractBitmap
copyInvert(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
copyLowest(int) - Method in interface etomica.graph.model.Bitmap: Creates an instance-compatible copy of lowest numBits bits of this bitmap.
copyLowest(int) - Method in class etomica.graph.model.impl.AbstractBitmap
CopyOfOrthogonalPolynomial - Class in etomica.densityofstate
CopyOfOrthogonalPolynomial() - Constructor for class etomica.densityofstate.CopyOfOrthogonalPolynomial
copyright - Static variable in class org.jmol.viewer.JmolConstants
copyTo(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagram
core - Static variable in class etomica.models.co2.P2CO2H2OWheatley
core - Static variable in class etomica.models.water.P2WaterSzalewicz
core - Variable in class etomica.models.water.PNWaterGCPM
core(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate core(n).
core() - Method in class etomica.veos.bigdecimal.Ifactor: The square-free part.
core_1 - Variable in class etomica.graph.isomorphism.AbstractSearchState
core_2 - Variable in class etomica.graph.isomorphism.AbstractSearchState
core_len - Variable in class etomica.graph.isomorphism.AbstractSearchState
coreCluster - Variable in class etomica.virial.ClusterSumMultibodyShell
coreCluster - Variable in class etomica.virial.ClusterSumShell
coreCO - Static variable in class etomica.models.co2.P2CO2H2OWheatley
coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBonding
coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellSurface
coreDiameter - Variable in class etomica.modules.mu.P2SquareWellOneSide
coreDiameter - Variable in class etomica.potential.P2DoubleWell
coreDiameter - Variable in class etomica.potential.P2PenetrableSphere
coreDiameter - Variable in class etomica.potential.P2SquareWell
coreDiameter - Variable in class etomica.potential.P2SquareWellRobust
coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBonding
coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellSurface
coreDiameterSquared - Variable in class etomica.modules.mu.P2SquareWellOneSide
coreDiameterSquared - Variable in class etomica.potential.P2DoubleWell
coreDiameterSquared - Variable in class etomica.potential.P2PenetrableSphere
coreDiameterSquared - Variable in class etomica.potential.P2PenetrableSquareWell
coreDiameterSquared - Variable in class etomica.potential.P2SquareWell
coreDiameterSquared - Variable in class etomica.potential.P2SquareWellRobust
coreFac - Variable in class etomica.models.co2.PNCO2GCPM
coreFac - Variable in class etomica.models.co2.PNGCPM
cornerData - Variable in class etomica.util.Grabber
CornerData() - Constructor for class etomica.util.Grabber.CornerData
CornerSetListener(Grabber, Grabber.ActionCornerSetter, int) - Constructor for class etomica.util.Grabber.CornerSetListener
corrector() - Method in class etomica.integrator.IntegratorGear4
corrector() - Method in class etomica.integrator.IntegratorGear4NPH
correlationSum - Variable in class etomica.data.AccumulatorAverageCollapsing
correlationSum - Variable in class etomica.data.AccumulatorAverageFixed
correlationSum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
corrugationButton - Variable in class etomica.modules.sam.SamGraphic
cos() - Method in class etomica.math.Complex: Cosine of this Complex number (doesn't change this Complex number).
cos(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Trigonometric cosine.
cos1m2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
cos1m2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
cos2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
cos2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
cosDtheta - Variable in class etomica.dimer.IntegratorDimerMin
cosg - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
cosg - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
cosh() - Method in class etomica.math.Complex: Hyperbolic cosine of this Complex number (doesn't change this Complex number).
cosh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The hyperbolic cosine.
coskrj - Variable in class etomica.potential.EwaldSummation
cosNominalTheta - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
cosNTheta - Variable in class etomica.potential.P3CPSNonAdditiveHe
cosNTheta - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
cosTheta - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
cosThetaConstraint - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
cosThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
cosThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
cosThetaSum - Variable in class etomica.potential.P3CPSNonAdditiveHe
cosThetaSum - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
cot(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The trigonometric co-tangent.
cot(double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: trigonometric cot.
Coulomb - Class in etomica.units: The coulomb unit of electrical charge.
count - Variable in class etomica.box.BoxMoleculeCountEvent
count - Variable in class etomica.data.AccumulatorAverage
count - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
count - Variable in class etomica.data.AccumulatorAverageBlockless
count - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
count - Variable in class etomica.data.AccumulatorAverageCollapsingLog
count - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
count - Static variable in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
count - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
count - Variable in class etomica.normalmode.HSNPT.ActionSummer
count - Variable in class etomica.normalmode.MeterOverlapSwitch
count - Variable in class etomica.normalmode.WriteS
Count - Class in etomica.units: Unit class for the number, or quantity, of something.
count - Variable in class etomica.util.HistogramNotSoSimple
count - Static variable in class etomica.virial.MeterVirialIC
count1 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
countEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2Site
countEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2SiteRho
countEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
counter - Variable in class etomica.atom.iterator.ANIntergroupCoupled
counter - Variable in class etomica.atom.iterator.ANIntergroupExchange
counter - Variable in class etomica.atom.iterator.ANIntragroupExchange
counter - Variable in class etomica.dimer.IntegratorDimerMin
counter - Variable in class etomica.dimer.IntegratorDimerRT
counter - Variable in class etomica.models.nitrogen.PRotConstraint
counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
counter - Variable in class etomica.models.oneDHardRods.MeterWidomMode
counter - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
counter - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
countMolecules(String) - Static method in class etomica.potential.PotentialEmul
counts - Variable in class etomica.metastable.MeterDensityDistribution
counts - Variable in class etomica.util.HistogramDiscrete
counts - Variable in class etomica.util.HistogramNotSoSimple
counts - Variable in class etomica.util.HistogramSimple
coupledMove - Variable in class etomica.models.hexane.TestHexane
coupledMove - Variable in class etomica.models.hexane.TestHexaneFileConfig
coupledMove - Variable in class etomica.models.hexane.TestSetToUHexane
covalent - Static variable in class org.jmol.script.Token
covalentMars - Static variable in class org.jmol.util.Elements: Default table of covalent Radii stored as a short mar ...
covar - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
covar - Variable in class etomica.util.numerical.NonLinearCurveFitting
COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance
covariance - Variable in class etomica.data.AccumulatorAverageCovariance
covSum - Variable in class etomica.data.AccumulatorAverageCovariance
cp - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
cPairID - Variable in class etomica.virial.BoxCluster
cPairID - Variable in class etomica.virial.ClusterChainHS
cPairID - Variable in class etomica.virial.ClusterChainSoft
cPairID - Variable in class etomica.virial.ClusterCoupledFlipped
cPairID - Variable in class etomica.virial.ClusterCoupledFlippedPartial
cPairID - Variable in class etomica.virial.ClusterSinglyConnected
cPairID - Variable in class etomica.virial.ClusterSum
cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
cPairID - Variable in class etomica.virial.ClusterWheatleyHS
cPairID - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
cPairID - Variable in class etomica.virial.ClusterWheatleySoft
cPairID - Variable in class etomica.virial.ClusterWheatleySoftBD
cPairSet - Variable in class etomica.virial.BoxCluster
cPairSetTmp - Variable in class etomica.virial.BoxCluster
cPairTrialSet - Variable in class etomica.virial.BoxCluster
crank - Variable in class etomica.models.hexane.TestHexane
crank - Variable in class etomica.models.hexane.TestHexaneFileConfig
create - Static variable in class org.jmol.script.Token
createAndShowGUI() - Method in class etomica.units.UnitGraphics
createArrayOfArrayList(int) - Static method in class org.jmol.util.ArrayUtil: Helper method for creating a List<T>[]without warnings.
createArrayOfHashtable(int) - Static method in class org.jmol.util.ArrayUtil: Helper method for creating a Map<K, V>[] without warnings.
createBitmap(String) - Static method in class etomica.graph.model.BitmapFactory
createBitmap(byte[]) - Static method in class etomica.graph.model.BitmapFactory
createBitmap(byte, boolean) - Static method in class etomica.graph.model.BitmapFactory
createCoefficient() - Static method in class etomica.graph.model.GraphFactory
createDecimalSliderStandardLabels(double) - Method in class etomica.graphics.DecimalSlider
createDisplayBoxPaintAction(IBox) - Method in class etomica.graphics.SimulationGraphic
createEdge(byte) - Static method in class etomica.graph.model.GraphFactory
createEdge(byte, char) - Static method in class etomica.graph.model.impl.EdgeImpl
createEdges() - Method in class etomica.graph.model.impl.GraphImpl
createEllipsoidShades() - Static method in class org.jmol.util.Shader
createFieldNode(byte, char) - Static method in class etomica.graph.model.impl.NodeImpl
createFont3D(int, int, float, float, ApiPlatform, Object) - Static method in class org.jmol.util.JmolFont
createGeodesic(int) - Static method in class org.jmol.util.Geodesic
createGraph(byte, Bitmap) - Static method in class etomica.graph.model.GraphFactory
createGraph(byte, byte, Bitmap) - Static method in class etomica.graph.model.GraphFactory
createGraph(byte) - Static method in class etomica.graph.model.GraphFactory
createGraph(Node[]) - Static method in class etomica.graph.model.GraphFactory
createImage(Object) - Method in interface org.jmol.api.ApiPlatform: can be ignored (return null) if platform cannot save images
createImage(Object) - Method in class org.jmol.awt.Platform: could be byte[] (from ZIP file) or String (local file name) or URL
createImageIcon(String) - Static method in class etomica.virial.GUI.models.ViewSpeciesSelection
createImageIcon(String) - Static method in class etomica.virial.GUI.views.ViewSpeciesSelection
createInnerIterator() - Method in class etomica.graph.iterators.CartesianIterator
createInnerIterator() - Method in class etomica.graph.iterators.PartitionedIterator
createInnerPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
createInstance(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap: Creates an instance of the implementing class based on the given parameters.
createInstance(int) - Method in class etomica.graph.model.impl.AbstractBitmap
createInstance(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
createInstance(int) - Method in class etomica.graph.model.impl.BitmapOfLong
createInstance(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
createInstance(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
createIntegrators() - Method in class etomica.kmc.IntegratorKMC
createIntegrators() - Method in class etomica.kmc.IntegratorKMCCluster
createNode(byte) - Static method in class etomica.graph.model.GraphFactory
createNode(byte, boolean) - Static method in class etomica.graph.model.GraphFactory
createNode(byte, char, char) - Static method in class etomica.graph.model.GraphFactory
createNode(byte, char, char) - Static method in class etomica.graph.model.impl.NodeImpl
createOffScreen(int, int) - Method in class etomica.graphics.DisplayCanvas
createOuterIterator() - Method in class etomica.graph.iterators.CartesianIterator
createOuterIterator() - Method in class etomica.graph.iterators.IsomorphismPrefilteredPartitionedIterator
createOuterIterator() - Method in class etomica.graph.iterators.PartitionedIterator
createOuterPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
createOutputDir(File) - Method in class etomica.graph.view.rasterizer.SVGConverter: Creates directories for output files if needed.
createReverseEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
createReverseEdges() - Method in interface etomica.graph.model.Graph
createReverseEdges() - Method in class etomica.graph.model.impl.GraphImpl
createRootNode(byte, char) - Static method in class etomica.graph.model.impl.NodeImpl
createSpecies() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
createSpeciesFactory() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
createThreads() - Method in class etomica.threads.AtomDecompositionMD
createView(String, Set<Graph>) - Static method in class etomica.graph.viewer.ClusterViewer
crep - Variable in class etomica.potential.P2HydrogenHinde
crep - Variable in class etomica.potential.P2HydrogenHindeAtomic
CRINGS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
CRINGS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
criterion - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
criterion - Variable in class etomica.modules.render.RenderMD
criterion - Variable in class etomica.potential.PotentialGroup
criterion3 - Variable in class etomica.modules.sam.Sam
CriterionAdapter - Class in etomica.nbr: Wraps another criterion while adding additional criteria to the acceptance decision.
CriterionAdapter(NeighborCriterion) - Constructor for class etomica.nbr.CriterionAdapter: Constructs criterion that wraps the given criterion.
CriterionAdapterMolecular - Class in etomica.nbr.molecule: Wraps another criterion while adding additional criteria to the acceptance decision.
CriterionAdapterMolecular(NeighborCriterionMolecular) - Constructor for class etomica.nbr.molecule.CriterionAdapterMolecular: Constructs criterion that wraps the given criterion.
CriterionAll - Class in etomica.nbr: Specifies that all atoms pairs are to be considered neighbors.
CriterionAll() - Constructor for class etomica.nbr.CriterionAll
CriterionAllMolecular - Class in etomica.nbr.molecule: Specifies that all atoms pairs are to be considered neighbors.
CriterionAllMolecular() - Constructor for class etomica.nbr.molecule.CriterionAllMolecular
CriterionBondedSimple - Class in etomica.nbr
CriterionBondedSimple(NeighborCriterion) - Constructor for class etomica.nbr.CriterionBondedSimple
CriterionCar(ParseObj, IBox) - Constructor for class etomica.modules.render.RenderMD.CriterionCar
CriterionInterMolecular - Class in etomica.nbr: Pair criterion that judges whether two atoms are or are not in the same molecule.
CriterionInterMolecular(NeighborCriterion) - Constructor for class etomica.nbr.CriterionInterMolecular: Constructs criterion in default state such that intramolecular pairs are rejected, and intermolecular pairs are accepted.
CriterionMolecular - Class in etomica.nbr: Pair criterion that judges whether two atoms are or are not in the same molecule.
CriterionMolecular(NeighborCriterion) - Constructor for class etomica.nbr.CriterionMolecular: Constructs criterion in default state such that intramolecular pairs are rejected, and intermolecular pairs are accepted.
CriterionMolecularNonAdjacent - Class in etomica.nbr: Pair criterion that judges whether two atoms are or are not in the same molecule, and whether or not they are separated by a minimum number of bonds.
CriterionMolecularNonAdjacent(NeighborCriterion) - Constructor for class etomica.nbr.CriterionMolecularNonAdjacent
CriterionNone() - Constructor for class etomica.modules.colloid.ColloidSim.CriterionNone
CriterionNone - Class in etomica.nbr
CriterionNone() - Constructor for class etomica.nbr.CriterionNone
CriterionPositionWall - Class in etomica.nbr: Simple neighbor criterion based on distance moved by a leaf atom since the last update.
CriterionPositionWall(ISimulation) - Constructor for class etomica.nbr.CriterionPositionWall
CriterionPositionWall.DoubleWrapper - Class in etomica.nbr
CriterionSimple - Class in etomica.nbr: Simple neighbor criterion based on distance moved by a leaf atom since the last update.
CriterionSimple(ISimulation, ISpace, double, double) - Constructor for class etomica.nbr.CriterionSimple
CriterionSimpleMolecular - Class in etomica.nbr.molecule: Simple neighbor criterion based on distance between the two molecules If the molecule moves further than r^2; the update method will kick in to update the neighborlist.
CriterionSimpleMolecular(ISimulation, ISpace, double, double) - Constructor for class etomica.nbr.molecule.CriterionSimpleMolecular
CriterionSpecies - Class in etomica.nbr.molecule: Filters molecule to match a given species.
CriterionSpecies(NeighborCriterionMolecular, ISpecies) - Constructor for class etomica.nbr.molecule.CriterionSpecies
CriterionSpeciesPair - Class in etomica.nbr.molecule: Filters molecule pairs to match a given pair of Species.
CriterionSpeciesPair(NeighborCriterionMolecular, ISpecies, ISpecies) - Constructor for class etomica.nbr.molecule.CriterionSpeciesPair
CriterionTether3 - Class in etomica.modules.sam: Returns first leaf atom of each polymer molecule and the atom its bonded to.
CriterionTether3(ISimulation, ISpecies, IAtomType) - Constructor for class etomica.modules.sam.CriterionTether3
CriterionType - Class in etomica.nbr: Filters atoms to match a given AtomType.
CriterionType(NeighborCriterion, IAtomType) - Constructor for class etomica.nbr.CriterionType
CriterionTypePair - Class in etomica.nbr: Filters atoms pairs to match a given pair of AtomTypes.
CriterionTypePair(NeighborCriterion, IAtomType, IAtomType) - Constructor for class etomica.nbr.CriterionTypePair
CriterionTypesCombination - Class in etomica.nbr: Filters AtomSets to match a given set of AtomTypes.
CriterionTypesCombination(NeighborCriterion, IAtomType[]) - Constructor for class etomica.nbr.CriterionTypesCombination
CriterionTypesMulti - Class in etomica.nbr: Filters AtomSets to match a given set of AtomTypes.
CriterionTypesMulti(NeighborCriterion, IAtomType[]) - Constructor for class etomica.nbr.CriterionTypesMulti
criterionWallMonomer - Variable in class etomica.modules.colloid.ColloidSim
criticalRho_LJ - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
criticalRho_SF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
criticalT_LJ - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
criticalT_SF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
cross - Static variable in class org.jmol.script.Token
cross(Vector3f, Vector3f) - Method in class org.jmol.util.Vector3f: Sets this vector to be the vector cross product of vectors v1 and v2.
crossPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
crossVector - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
CrystalViewer - Class in etomica.modules.crystalviewer
CrystalViewer() - Constructor for class etomica.modules.crystalviewer.CrystalViewer
CrystalViewer.Applet - Class in etomica.modules.crystalviewer
cs - Variable in class etomica.dimer.P1LepsHarmonic
csp - Static variable in class etomica.potential.P2HydrogenPatkowski
csp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
cspIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
cten - Variable in class etomica.potential.P2HydrogenHinde
cten - Variable in class etomica.potential.P2HydrogenHindeAtomic
cType - Variable in class etomica.AlkaneEH.SpeciesMethane
cType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
cType - Variable in class etomica.models.rowley.SpeciesEthanol
cType - Variable in class etomica.models.water.SpeciesWater4PCOM
cType - Variable in class etomica.paracetamol.SpeciesParacetamol
cType - Variable in class etomica.virial.SpeciesAnthracene3site464
cType - Variable in class etomica.virial.SpeciesAnthracene3site545
cType - Variable in class etomica.virial.SpeciesMethane
cType - Variable in class etomica.virial.SpeciesPh3site464
cType - Variable in class etomica.virial.SpeciesPh3site545
cType - Variable in class etomica.virial.SpeciesTraPPEAnthracene
cType - Variable in class etomica.virial.SpeciesTraPPECO2
cType - Variable in class etomica.virial.SpeciesTraPPENaphthalene
cType - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
cu - Variable in class etomica.dimer.EnergyMap
cu - Variable in class etomica.meam.MEAM_MC
cu - Variable in class etomica.meam.MEAMMd3D
Cu - Static variable in class etomica.meam.ParameterSetMEAM
cu - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
Cu3Sn - Static variable in class etomica.meam.ParameterSetMEAM
cuAdatom - Variable in class etomica.dimer.EnergyMap
cuB - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
Cube - Class in etomica.math.geometry: A geometric cube.
Cube(ISpace) - Constructor for class etomica.math.geometry.Cube: Constructs a cube of unit size.
Cube(ISpace, double) - Constructor for class etomica.math.geometry.Cube: Constructs a cube with edge length having the given value.
cubeRoot(double) - Static method in class etomica.space3d.Vector3D
cubeVertexOffsets - Static variable in class org.jmol.util.BoxInfo
cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
CubicCentimeter - Class in etomica.units: The cubic centimeter unit of volume, cm^3.
CubicLattice - Interface in etomica.lattice: Lattice or crystal with cubic symmetry, such that its spatial size can be characterized by a single value, the lattice constant.
CubicMeter - Class in etomica.units: The cubic meter unit of volume, m^3.
Cuboid - Class in etomica.math.geometry: A polyhedron composed of three pairs of rectangular faces placed opposite each other and joined at right angles, also known as a rectangular parallelepiped.
Cuboid(ISpace) - Constructor for class etomica.math.geometry.Cuboid: Constructs a cuboid with equal faces of unit size (a cube).
Cuboid(ISpace, double, double, double) - Constructor for class etomica.math.geometry.Cuboid: Constructs a cuboid with edges of lengths having the given values.
cuFix - Variable in class etomica.dimer.EnergyMap
cuFixedB - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
cumint - Variable in class etomica.mappedvirial.MappedUpotential
cumint(double) - Method in class etomica.mappedvirial.MappedUpotential
cumint - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
cumint(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
cumint - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
cumint(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
CURRENT - Static variable in class etomica.action.activity.Controller.ActionStatus
Current - Class in etomica.units: The dimension for electrical current.
current() - Method in class etomica.units.systems.CGS
current() - Method in class etomica.units.systems.LJ
current() - Method in class etomica.units.systems.MKS
current() - Method in class etomica.units.systems.UnitSystem
current() - Method in class etomica.units.systems.UnitSystem.Sim
currentAction - Variable in class etomica.action.activity.ActivityGroupSeries
currentBlockSum - Variable in class etomica.data.AccumulatorAverageCollapsing
currentBlockSum - Variable in class etomica.data.AccumulatorAverageFixed
currentBlockSum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
currentBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
currentCores - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
currentKineticEnergy - Variable in class etomica.integrator.IntegratorMD
currentLattice - Variable in class etomica.modules.crystalviewer.LatticeEditor
currentlocalpath - Static variable in class org.jmol.script.Token
currentlyRendering() - Method in class org.jmol.g3d.Graphics3D
currentPotentialEnergy - Variable in class etomica.integrator.IntegratorBox
currentTime - Variable in class etomica.integrator.IntegratorMD
currentWells - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
cursor - Variable in class etomica.atom.iterator.ApiIndexList
cursor - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple: Index of element to be returned by subsequent call to next.
cursor - Variable in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Index of element to be returned by subsequent call to next.
cursor - Variable in class etomica.atom.iterator.TripletInnerSequential
cursor - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
cursor - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
cursor - Variable in class etomica.lattice.RectangularLatticeNbrIterator
cursor - Variable in class etomica.modules.sam.CriterionTether3
cursor - Variable in class etomica.util.HistoryCollapsing
CURSOR_CROSSHAIR - Static variable in class org.jmol.viewer.JmolConstants
CURSOR_DEFAULT - Static variable in class org.jmol.viewer.JmolConstants
CURSOR_HAND - Static variable in class org.jmol.viewer.JmolConstants
CURSOR_MOVE - Static variable in class org.jmol.viewer.JmolConstants
CURSOR_WAIT - Static variable in class org.jmol.viewer.JmolConstants
CURSOR_ZOOM - Static variable in class org.jmol.viewer.JmolConstants
curvature - Variable in class etomica.dimer.IntegratorDimerRT
customVF - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
cutoff - Variable in class etomica.modules.dcvgcmd.P1WCAWall
cutoff - Variable in class etomica.modules.droplet.AtomFilterLiquid
cutoff - Variable in class etomica.modules.sam.P1WCAWall
cutoff - Variable in class etomica.potential.P2ReactionFieldDipole
cutoff - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
cutoff2 - Variable in class etomica.modules.sam.P1WCAWall
cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipole
cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
cutoff2 - Variable in class etomica.rotation.P2LJDipole
cutoffRatio - Variable in class etomica.potential.P2MoleculeTruncated
cutoffRatio - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
cutoffSq - Variable in class etomica.modules.droplet.AtomFilterLiquid
cVec - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
cVector - Variable in class etomica.action.BoxInflateAnisotropic
cVectorOld - Variable in class etomica.action.BoxInflateAnisotropic
CVisitor - Class in etomica.graph.traversal: This TraversalVisitor visits nodes and keeps track of biconnected components.
CVisitor(List<List<Byte>>) - Constructor for class etomica.graph.traversal.CVisitor
CYAN - Static variable in class org.jmol.util.Colix
cycleDrawBoundaryType() - Method in class g3dsys.images.ImageShell: Cycles to the next boundary drawing style
cycles - Variable in class etomica.modules.osmosis.Osmosis
CYLINDER - Static variable in class g3dsys.control.G3DSys
CYLINDER - Static variable in class g3dsys.images.Bond

D

D() - Method in class etomica.config.ConfigurationLattice.MyLattice
D - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
d - Variable in class etomica.dimer.SimDimerLJadatom
d - Variable in class etomica.dimer.SimDimerMEAMadatom
d - Variable in class etomica.dimer.SimDimerMEAMGB
D - Variable in class etomica.integrator.IntegratorGear4NPH
D - Variable in class etomica.integrator.mcmove.MCMoveVolume
d - Variable in class etomica.kmc.SimKMCMEAMadatom
D() - Method in interface etomica.lattice.AbstractLattice: Dimension of the lattice.
D() - Method in class etomica.lattice.BravaisLattice
D() - Method in class etomica.lattice.BravaisLatticeCrystal: Returns the spatial dimension + 1.
D - Variable in class etomica.lattice.crystal.Primitive
D - Variable in class etomica.lattice.RectangularLattice
D() - Method in class etomica.lattice.RectangularLattice
D - Variable in class etomica.lattice.RectangularLatticeNbrIterator
D() - Method in class etomica.lattice.RectangularLatticeNbrIterator
D() - Method in class etomica.math.geometry.Hypersphere
D - Variable in class etomica.math.geometry.Polytope
D() - Method in class etomica.math.geometry.Polytope: The dimension of this polytope, which is not necessarily the dimension of the space it is embedded in.
D() - Method in interface etomica.math.geometry.Shape: Returns the spatial dimension of the shape.
D - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
D - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
D - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
D - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
D - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
D - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
D - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
D - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
D - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
D - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
D - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
d - Variable in class etomica.modules.rheology.MeterNormalStress
D - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
D - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
D - Variable in class etomica.normalmode.SimBennet.SimBennetParam
D - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
D - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
D - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
D - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
D - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
D - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
D() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
D() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
d(int, double, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
D - Static variable in class etomica.potential.P3HydrogenManzhos
d - Static variable in class etomica.potential.P3HydrogenManzhos
D() - Method in interface etomica.space.ISpace: The dimension of this space.
D() - Method in class etomica.space.Space
D() - Method in interface etomica.space.Tensor
D() - Method in class etomica.space1d.Space1D
D() - Method in class etomica.space1d.Tensor1D
D() - Method in class etomica.space2d.Space2D
D() - Method in class etomica.space2d.Tensor2D
D() - Method in class etomica.space3d.Space3D
D() - Method in class etomica.space3d.Tensor3D
D() - Method in class etomica.spaceNd.TensorND
d - Variable in class etomica.util.numerical.PadeApproximation.VirialParam
d0 - Variable in class etomica.potential.P3HydrogenManzhos
d2 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
d2dfac - Variable in class etomica.util.numerical.AkimaSplineSmoother
d2f(int[], double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
d2fac - Variable in class etomica.util.numerical.AkimaSplineSmoother
d2phi_du2(int[]) - Method in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
d2phi_du2(int[], int[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
d2phi_du2(int[], double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
d2phi_du2(int[], int[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
d2r - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
d2sum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
d2tot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
d2tot - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
d2tot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
d2tot - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
d2u(double) - Method in class etomica.models.rowley.P2RepRowley: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.modules.droplet.P2Cohesion
d2u(double) - Method in class etomica.potential.P1HydrogenMielke
d2u(double) - Method in interface etomica.potential.P1IntraMolecular
d2u(double) - Method in class etomica.potential.P2Anharmonic: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2ArgonAziz1993: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
d2u(double) - Method in class etomica.potential.P2Dreiding: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Electrostatic
d2u(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
d2u(double) - Method in class etomica.potential.P2Exp6: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Exp6Buckingham: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Fene: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Harmonic: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2HePCKLJS: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2HeSimplified: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
d2u(double) - Method in class etomica.potential.P2LennardJones: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2LennardJonesDreiding: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2LJQQ
d2u(double) - Method in class etomica.potential.P2ModifiedMorse: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2Morse: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2QChemInterpolated: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2SoftSphere: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the 2nd derivative (r^2 d^2u/dr^2) of the wrapped potential if the separation is less than the cutoff value
d2u(double) - Method in class etomica.potential.P2WCA: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.potential.Potential2SoftSpherical: The second derivative of the pair energy, times the square of the separation: r^2 d^2u/dr^2.
d2u(double) - Method in class etomica.virial.P1IntraLambda
d2u(double) - Method in class etomica.yukawa.P2HC2Yukawa
d2u(double) - Method in class etomica.yukawa.P2Yukawa: r^2 * d^2u/dr^2 method.
d2uCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc: Uses result from integration-by-parts to evaluate integral of r2 d2u/dr2 using integral of u.
d3dfac - Variable in class etomica.util.numerical.AkimaSplineSmoother
d3fac - Variable in class etomica.util.numerical.AkimaSplineSmoother
D4 - Static variable in class etomica.virial.cluster.Standard
D5 - Static variable in class etomica.virial.cluster.Standard
D6 - Static variable in class etomica.virial.cluster.Standard
da - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
da - Variable in class etomica.util.numerical.NonLinearCurveFitting
dab - Variable in class etomica.dimer.P1LepsHarmonic
dac - Variable in class etomica.dimer.P1LepsHarmonic
dAcc - Variable in class etomica.spin.Heisenberg
dadbSum - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
dadbSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
dadbSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
daDef - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
daDef - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
daDef - Variable in class etomica.normalmode.SimLJVacancy.LJParams
Dalton - Class in etomica.units
damp(int, double, double) - Method in class etomica.models.water.P2WaterSzalewicz
DampingParams() - Constructor for class etomica.potential.P2QChemInterpolated.DampingParams
DampingParams() - Constructor for class etomica.potential.P3AdditiveQChem.DampingParams
DampingParams() - Constructor for class etomica.potential.P3QChem.DampingParams
DampingParams() - Constructor for class etomica.virial.B3ForSphericallySymmetricU.DampingParams
DASH_MAP - Static variable in interface etomica.graph.model.Metadata
daSpan - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
data - Variable in class etomica.data.AccumulatorCounter
data - Variable in class etomica.data.DataDump
data - Variable in class etomica.data.DataProcessorChemicalPotential
data - Variable in class etomica.data.DataProcessorFunction
data - Variable in class etomica.data.DataProcessorInterfacialTension
data - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
data - Variable in class etomica.data.DataSourceScalar
data - Variable in class etomica.data.DataSourceTensorVirialHard
data - Variable in class etomica.data.meter.MeterDihedralAngle
data - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
data - Variable in class etomica.data.meter.MeterHyperVirial
data - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
data - Variable in class etomica.data.meter.MeterPressureTensor
data - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
data - Variable in class etomica.data.meter.MeterProfileByAtoms
data - Variable in class etomica.data.meter.MeterProfileByVolume
data - Variable in class etomica.data.meter.MeterRDF
data - Variable in class etomica.data.meter.MeterRDFPC
data - Variable in class etomica.data.types.DataGroup
data - Variable in class etomica.freeenergy.npath.DataSourceEnergies
data - Variable in class etomica.gaussianwork.MeterBoltzmannA
data - Variable in class etomica.gaussianwork.MeterBoltzmannB
data - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
data - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
data - Variable in class etomica.liquidLJ.DataProcessorReweight
data - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
data - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
data - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
data - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
data - Variable in class etomica.liquidLJ.MeterPU
data - Variable in class etomica.liquidLJ.MeterPUCut
data - Variable in class etomica.liquidLJ.MeterPUCutLS
data - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
data - Variable in class etomica.mappedvirial.MeterMeanForce
data - Variable in class etomica.metastable.DataProcessorXY
data - Variable in class etomica.models.nitrogen.MeterBoltzmann
data - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
data - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
data - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
data - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
data - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
data - Variable in class etomica.modules.chainequilibrium.MeterChainLength
data - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg
data - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg2
data - Variable in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
data - Variable in class etomica.modules.droplet.MeterDeformation
data - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
data - Variable in class etomica.modules.entropylottery.EntropyProcessor
data - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
data - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
data - Variable in class etomica.modules.interfacial.MeterOrientation
data - Variable in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
data - Variable in class etomica.modules.mu.DataSourceWallPressureMu
data - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
data - Variable in class etomica.modules.multiharmonic.DataProcessorBias
data - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
data - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
data - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
data - Variable in class etomica.modules.rosmosis.MeterFlux
data - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
data - Variable in class etomica.modules.sam.MeterTilt
data - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
data - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
data - Variable in class etomica.normalmode.DataSourceFE
data - Variable in class etomica.normalmode.DataSourceFEHistogram
data - Variable in class etomica.normalmode.DataSourceImposedFEFit
data - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
data - Variable in class etomica.normalmode.DataSourcePMu
data - Variable in class etomica.normalmode.DataSourcePN
data - Variable in class etomica.normalmode.MeterBoltzmann
data - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
data - Variable in class etomica.normalmode.MeterBoltzmannHTTP
data - Variable in class etomica.normalmode.MeterBoltzmannTarget
data - Variable in class etomica.normalmode.MeterDADB
data - Variable in class etomica.normalmode.MeterDDP
data - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
data - Variable in class etomica.normalmode.MeterDirectSamplingTarget
data - Variable in class etomica.normalmode.MeterDP
data - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
data - Variable in class etomica.normalmode.MeterOverlapSwitch
data - Variable in class etomica.normalmode.MeterPlaneSlip
data - Variable in class etomica.normalmode.MeterSamplingHarmonic
data - Variable in class etomica.normalmode.MeterSamplingTarget
data - Variable in class etomica.normalmode.MeterSolidDA
data - Variable in class etomica.normalmode.MeterSolidDACut
data - Variable in class etomica.normalmode.MeterSolidMirror
data - Variable in class etomica.normalmode.MeterSolidProps
data - Variable in class etomica.normalmode.MeterSolidPropsLJ
data - Variable in class etomica.normalmode.MeterTargetTP
data - Variable in class etomica.normalmode.MeterTilt
data - Variable in class etomica.normalmode.MeterTiltHistogram
data - Variable in class etomica.normalmode.MeterTiltRotation
data - Variable in class etomica.normalmode.MeterTiltRotationHistogram
data - Variable in class etomica.normalmode.MeterTiltRotationStdev
data - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
data - Variable in class etomica.normalmode.MeterWorkBennetTarget
data - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
data - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
data - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
data - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
data - Variable in class etomica.normalmode.MeterWorkTargetBennet
data - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
data - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
data - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
data - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
data - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
data - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
data - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
data - Variable in class etomica.overlap.MeterOverlap
data - Variable in class etomica.surfacetension.SurfaceTensionMapped
data - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
data - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
data - Static variable in class org.jmol.script.Token
DataAccumulator - Class in etomica.data: DataProcessor that accumulates and transforms given data and intermittently transmits processed data to other DataSink(s).
DataAccumulator() - Constructor for class etomica.data.DataAccumulator: Constructs accumulator with no initial DataSink.
DataAccumulator(IDataSink) - Constructor for class etomica.data.DataAccumulator: Constructs DataAccumulator with the given DataSink.
DataArrayWriter - Class in etomica.data: A DataWriter that writes out data as a table with optional column headings
DataArrayWriter() - Constructor for class etomica.data.DataArrayWriter
databases - Static variable in class org.jmol.viewer.JmolConstants
DataCasterJudgeFunction() - Constructor for class etomica.graphics.DisplayPlot.DataCasterJudgeFunction
DataCasterJudgeTable() - Constructor for class etomica.data.DataSinkTable.DataCasterJudgeTable
dataChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSet: Notifies the DataSet that new Data has arrived for the given psuedo DataSink.
dataChanged(DataSet) - Method in interface etomica.data.DataSetListener: Method called when one or more pieces of data have changed.
dataChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSinkTable
dataChanged(DataSet) - Method in class etomica.graphics.DisplayPlot: Causes the display of the plot to be updated.
dataChanged(DataSet) - Method in class etomica.graphics.DisplayTable: Causes the display of the plot to be updated.
dataCountChanged(DataSet) - Method in interface etomica.data.DataSetListener: Method called when a Data object is added.
dataCountChanged(DataSet) - Method in class etomica.graphics.DisplayPlot: Updates the units array for the new column, using the default units.
dataCountChanged(DataSet) - Method in class etomica.graphics.DisplayTable: Updates the units array for any new or deleted columns, using the default units for new columns.
DataCutter - Class in etomica.zeolite
DataCutter(String, int) - Constructor for class etomica.zeolite.DataCutter
dataDistance - Variable in class etomica.virial.MeterSamplingWeight
DataDistributer - Class in etomica.data: DataSink that takes a Data object and pushes it to a dataSink chosen by an indexer.
DataDistributer(DataDistributer.Indexer, DataSplitter.IDataSinkFactory) - Constructor for class etomica.data.DataDistributer
DataDistributer.Indexer - Interface in etomica.data
DataDouble - Class in etomica.data.types: Data object wrapping a single mutable value of type double.
DataDouble() - Constructor for class etomica.data.types.DataDouble: Constructs a new instance with given descriptors.
DataDouble.DataInfoDouble - Class in etomica.data.types
DataDouble.DataInfoDoubleFactory - Class in etomica.data.types
DataDoubleArray - Class in etomica.data.types: Data object that wraps a mutable array of doubles.
DataDoubleArray(int) - Constructor for class etomica.data.types.DataDoubleArray: Constructs a new one-dimensional array of the given length.
DataDoubleArray(int[]) - Constructor for class etomica.data.types.DataDoubleArray: Constructs a new multidimensional array of the given shape.
DataDoubleArray(int[], double[]) - Constructor for class etomica.data.types.DataDoubleArray: Wraps the given array, xData in a DataDoubleArray of the given shape.
DataDoubleArray.DataInfoDoubleArray - Class in etomica.data.types
DataDoubleArray.DataInfoDoubleArrayFactory - Class in etomica.data.types
DataDoubleBDArray - Class in etomica.data.types: Data object that wraps a array of BigDecimals.
DataDoubleBDArray(int, int) - Constructor for class etomica.data.types.DataDoubleBDArray: Constructs a new one-dimensional array of the given length.
DataDoubleBDArray(int[], int) - Constructor for class etomica.data.types.DataDoubleBDArray: Constructs a new multidimensional array of the given shape.
DataDoubleBDArray.DataInfoDoubleBDArray - Class in etomica.data.types
DataDoubleBDArray.DataInfoDoubleBDArrayFactory - Class in etomica.data.types
DataDump - Class in etomica.data: DataPump acts both as a DataSink and a DataSource.
DataDump() - Constructor for class etomica.data.DataDump
dataDy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
dataDy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
dataDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
dataDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
dataDy3 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
dataEVec - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
dataEy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
dataEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
DataFork - Class in etomica.data: DataSink that takes a data stream and forwards it across multiple sinks.
DataFork() - Constructor for class etomica.data.DataFork: Constructs with no initial DataSinks.
DataFork(IDataSink[]) - Constructor for class etomica.data.DataFork: Constructs to forward data to the given sinks.
DataFunction - Class in etomica.data.types: Collects two or more DataDoubleArray instances, and organizes them into "dependent" and "independent" subgroups.
DataFunction(int[], double[]) - Constructor for class etomica.data.types.DataFunction: Forms a DataFunction using the given independent and dependent data instances.
DataFunction(int[]) - Constructor for class etomica.data.types.DataFunction: Forms a DataFunction with the given array shape.
DataFunction.DataInfoFunction - Class in etomica.data.types
DataFunction.DataInfoFunctionFactory - Class in etomica.data.types
dataGroup - Variable in class etomica.data.AccumulatorAverage
dataGroup - Variable in class etomica.data.AccumulatorAverageBlockless
DataGroup - Class in etomica.data.types: Gathers one or more Data instances into a single Data object.
DataGroup(IData[]) - Constructor for class etomica.data.types.DataGroup: Forms a data group from the given array of data objects.
dataGroup - Variable in class etomica.normalmode.MeterTiltRotationHistogram
DataGroup.DataInfoGroup - Class in etomica.data.types
DataGroup.DataInfoGroupFactory - Class in etomica.data.types
DataGroupFilter - Class in etomica.data: Extracts one or more of the Data instances wrapped in a DataGroup.
DataGroupFilter(int) - Constructor for class etomica.data.DataGroupFilter: Creates a filter that will take the DataGroup element indicated by the index, counting from 0.
DataGroupFilter(int[]) - Constructor for class etomica.data.DataGroupFilter: Creates a filter that will take the set of elements from the DataGroup corresponding to the given index values (with indexes counting from 0).
DataGroupSplitter - Class in etomica.data: DataSink that takes a DataGroup object and pushes each sub-Data object from the incoming DataGroup to a different stream.
DataGroupSplitter() - Constructor for class etomica.data.DataGroupSplitter
DataHistogram - Class in etomica.data: DataProcessor that creates a histogram from each piece of data that comes in.
DataHistogram(int, DoubleRange) - Constructor for class etomica.data.DataHistogram: Creates instance using HistogramSimple and specifying histograms having the given number of bins and the given range.
DataHistogram(Histogram) - Constructor for class etomica.data.DataHistogram: Creates instance using the given histogram.
dataInfo - Variable in class etomica.data.DataDistributer
dataInfo - Variable in class etomica.data.DataDump
dataInfo - Variable in class etomica.data.DataFork
DataInfo - Class in etomica.data: Object associated with a Data instance and which provides descriptive information about the data encapsulated in it.
DataInfo(String, Dimension) - Constructor for class etomica.data.DataInfo: Constructs new instance with descriptive label and dimension.
dataInfo - Variable in class etomica.data.DataProcessor
dataInfo - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
dataInfo - Variable in class etomica.data.DataSourceScalar
dataInfo - Variable in class etomica.data.DataSourceTensorVirialHard
dataInfo - Variable in class etomica.data.DataSplitter
dataInfo - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
dataInfo - Variable in class etomica.data.meter.MeterHyperVirial
dataInfo - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
dataInfo - Variable in class etomica.data.meter.MeterPressureTensor
dataInfo - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
dataInfo - Variable in class etomica.data.meter.MeterProfileByAtoms
dataInfo - Variable in class etomica.data.meter.MeterProfileByVolume
dataInfo - Variable in class etomica.freeenergy.npath.DataSourceEnergies
dataInfo - Variable in class etomica.gaussianwork.MeterBoltzmannA
dataInfo - Variable in class etomica.gaussianwork.MeterBoltzmannB
dataInfo - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
dataInfo - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
dataInfo - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
dataInfo - Variable in class etomica.liquidLJ.MeterPU
dataInfo - Variable in class etomica.liquidLJ.MeterPUCut
dataInfo - Variable in class etomica.liquidLJ.MeterPUCutLS
dataInfo - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection: Number of insertions attempted in each call to currentValue Default is 100
dataInfo - Variable in class etomica.mappedvirial.MeterMeanForce
dataInfo - Variable in class etomica.models.nitrogen.MeterBoltzmann
dataInfo - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
dataInfo - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
dataInfo - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
dataInfo - Variable in class etomica.models.oneDHardRods.MeterNMCBaskets
dataInfo - Variable in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
dataInfo - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
dataInfo - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
dataInfo - Variable in class etomica.modules.chainequilibrium.MeterChainLength
dataInfo - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg
dataInfo - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg2
dataInfo - Variable in class etomica.modules.droplet.MeterDeformation
dataInfo - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
dataInfo - Variable in class etomica.modules.interfacial.MeterOrientation
dataInfo - Variable in class etomica.modules.mu.DataSourceWallPressureMu
dataInfo - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorBias
dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
dataInfo - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
dataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
dataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
dataInfo - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
dataInfo - Variable in class etomica.modules.rosmosis.MeterFlux
dataInfo - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
dataInfo - Variable in class etomica.modules.sam.MeterTilt
dataInfo - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
dataInfo - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
dataInfo - Variable in class etomica.normalmode.DataSourceFE
dataInfo - Variable in class etomica.normalmode.DataSourceFEHistogram
dataInfo - Variable in class etomica.normalmode.DataSourceImposedFEFit
dataInfo - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
dataInfo - Variable in class etomica.normalmode.DataSourcePMu
dataInfo - Variable in class etomica.normalmode.DataSourcePN
dataInfo - Variable in class etomica.normalmode.MeterBoltzmann
dataInfo - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
dataInfo - Variable in class etomica.normalmode.MeterBoltzmannHTTP
dataInfo - Variable in class etomica.normalmode.MeterBoltzmannTarget
dataInfo - Variable in class etomica.normalmode.MeterDADB
dataInfo - Variable in class etomica.normalmode.MeterDDP
dataInfo - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
dataInfo - Variable in class etomica.normalmode.MeterDirectSamplingTarget
dataInfo - Variable in class etomica.normalmode.MeterDP
dataInfo - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
dataInfo - Variable in class etomica.normalmode.MeterOverlapSwitch
dataInfo - Variable in class etomica.normalmode.MeterPlaneSlip
dataInfo - Variable in class etomica.normalmode.MeterSamplingHarmonic
dataInfo - Variable in class etomica.normalmode.MeterSamplingTarget
dataInfo - Variable in class etomica.normalmode.MeterSolidDA
dataInfo - Variable in class etomica.normalmode.MeterSolidDACut
dataInfo - Variable in class etomica.normalmode.MeterSolidMirror
dataInfo - Variable in class etomica.normalmode.MeterSolidProps
dataInfo - Variable in class etomica.normalmode.MeterSolidPropsLJ
dataInfo - Variable in class etomica.normalmode.MeterTargetTP
dataInfo - Variable in class etomica.normalmode.MeterTilt
dataInfo - Variable in class etomica.normalmode.MeterTiltHistogram
dataInfo - Variable in class etomica.normalmode.MeterTiltRotation
dataInfo - Variable in class etomica.normalmode.MeterTiltRotationHistogram
dataInfo - Variable in class etomica.normalmode.MeterTiltRotationStdev
dataInfo - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
dataInfo - Variable in class etomica.normalmode.MeterWorkBennetTarget
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetBennet
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
dataInfo - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
dataInfo - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
dataInfo - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
dataInfo - Variable in class etomica.overlap.MeterOverlap
dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
dataInfoChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSet: Notifies the DataSet that new DataInfo has arrived for the given psuedo DataSink.
dataInfoChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSinkTable
DataInfoDouble(String, Dimension) - Constructor for class etomica.data.types.DataDouble.DataInfoDouble
DataInfoDoubleArray(String, Dimension, int[]) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
DataInfoDoubleArrayFactory(DataDoubleArray.DataInfoDoubleArray) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
DataInfoDoubleBDArray(String, Dimension, int[], int) - Constructor for class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
DataInfoDoubleBDArrayFactory(DataDoubleBDArray.DataInfoDoubleBDArray) - Constructor for class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
DataInfoDoubleFactory(DataDouble.DataInfoDouble) - Constructor for class etomica.data.types.DataDouble.DataInfoDoubleFactory
DataInfoFactory - Class in etomica.data: Interface for a mutable DataInfo factory.
DataInfoFactory(IEtomicaDataInfo) - Constructor for class etomica.data.DataInfoFactory: Creates a new instance using the info held by the template.
DataInfoFunction(String, Dimension, DataSourceIndependent) - Constructor for class etomica.data.types.DataFunction.DataInfoFunction
DataInfoFunctionFactory(DataFunction.DataInfoFunction) - Constructor for class etomica.data.types.DataFunction.DataInfoFunctionFactory
dataInfoGroup - Variable in class etomica.data.DataGroupSplitter
DataInfoGroup(String, Dimension, IEtomicaDataInfo[]) - Constructor for class etomica.data.types.DataGroup.DataInfoGroup
dataInfoGroup - Variable in class etomica.normalmode.MeterTiltRotationHistogram
DataInfoGroupFactory(DataGroup.DataInfoGroup) - Constructor for class etomica.data.types.DataGroup.DataInfoGroupFactory
DataInfoTable(String, IEtomicaDataInfo[], int, String[]) - Constructor for class etomica.data.types.DataTable.DataInfoTable
DataInfoTableFactory(DataTable.DataInfoTable) - Constructor for class etomica.data.types.DataTable.DataInfoTableFactory
DataInfoTensor(String, Dimension, ISpace) - Constructor for class etomica.data.types.DataTensor.DataInfoTensor
DataInfoTensorFactory(DataTensor.DataInfoTensor) - Constructor for class etomica.data.types.DataTensor.DataInfoTensorFactory
DataInfoVector(String, Dimension, ISpace) - Constructor for class etomica.data.types.DataVector.DataInfoVector
DataInfoVectorFactory(DataVector.DataInfoVector) - Constructor for class etomica.data.types.DataVector.DataInfoVectorFactory
dataInterval - Variable in class etomica.interfacial.LJMD.LJMDParams
dataInterval - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
DataLogger - Class in etomica.data: DataSink that manages a FileWriter and also listens to non-interval integrator events and sends appropriate data to a DataWriter.
DataLogger() - Constructor for class etomica.data.DataLogger
DataLogger.DataWriter - Interface in etomica.data: Interface for a DataSink that actually writes data to a file
dataOverlap - Variable in class etomica.normalmode.SimOverlapModule
DataOverlap - Class in etomica.overlap: Utility class for overlap sampling.
DataOverlap(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource) - Constructor for class etomica.overlap.DataOverlap
DataOverlap.DataSourceOverlapAvg - Interface in etomica.overlap: Interface for a class capable of return the average and uncertainty for a particular value of alpha.
DataOverlap.DataSourceOverlapAvgCollapsing - Class in etomica.overlap: Implementation of DataSourceOverlapLogAvg that retrieves data from a splitter whose data is dumped into different AccumulatorAverageCollapsingLog instances.
DataOverlap.DataSourceOverlapAvgCollapsingSplit - Class in etomica.overlap
DataOverlap.DataSourceOverlapAvgSimple - Class in etomica.overlap: Implementation of DataSourceOverlapAvg that retrieves data from a single AccumulatorAverage
DataOverlap.DataSourceOverlapLogAvg - Interface in etomica.overlap: Interface for a class capable of return the average and uncertainty as well as the log of the average and the uncertainty in the log, for a particular value of alpha.
DataOverlapCaching - Class in etomica.modules.multiharmonic.overlap: DataOverlap subclass that caches return values.
DataOverlapCaching(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource, IntegratorOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.DataOverlapCaching
DataPipe - Interface in etomica.data: Interface for an object through which data can flow.
DataPipeForked - Interface in etomica.data
DataPipeStressStrain(Sam) - Constructor for class etomica.modules.sam.SamGraphic.DataPipeStressStrain
DataProcessAHT(MultiharmonicGraphicMC.DataSourceUa, HistoryCollapsingDiscard) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
DataProcessor - Class in etomica.data: An object that receives Data, processes it, and pushes the result on to a DataSink.
DataProcessor() - Constructor for class etomica.data.DataProcessor
DataProcessorBias - Class in etomica.modules.multiharmonic: Data Processor which calculates the bias in the incoming data based on the true value of the free energy calculated from the
DataProcessorBias(DataSourceScalar) - Constructor for class etomica.modules.multiharmonic.DataProcessorBias
DataProcessorBoltzmannFactor - Class in etomica.normalmode
DataProcessorBoltzmannFactor() - Constructor for class etomica.normalmode.DataProcessorBoltzmannFactor
DataProcessorBounds - Class in etomica.modules.multiharmonic: Calculates upper or lower bound of the incoming data based on the standard deviation obtained from the accumulator.
DataProcessorBounds() - Constructor for class etomica.modules.multiharmonic.DataProcessorBounds
DataProcessorChemicalPotential - Class in etomica.data: DataProcessor that takes as input the average density and average Boltzmann factor profiles and calculates the chemical potential profile as the sum of the ideal gas contribution (kT ln()) and the excess chemical potential, (-kT ln()).
DataProcessorChemicalPotential() - Constructor for class etomica.data.DataProcessorChemicalPotential
DataProcessorCorrection(int) - Constructor for class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
DataProcessorCvMD - Class in etomica.meam
DataProcessorCvMD() - Constructor for class etomica.meam.DataProcessorCvMD
DataProcessorDyDLnx - Class in etomica.modules.multiharmonic: Calculates dy/dlnx vs.
DataProcessorDyDLnx() - Constructor for class etomica.modules.multiharmonic.DataProcessorDyDLnx
DataProcessorFoo() - Constructor for class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
DataProcessorForked - Class in etomica.data: A DataProcessor that can handle multiple sinks, passing the same Data to each.
DataProcessorForked() - Constructor for class etomica.data.DataProcessorForked
DataProcessorFunction - Class in etomica.data: Applies a simple scalar function to all elements of the Data that passes through.
DataProcessorFunction(IFunction) - Constructor for class etomica.data.DataProcessorFunction
DataProcessorInterfacialTension - Class in etomica.data: Data Processor that takes the virial components as input data and returns the interfacial tension.
DataProcessorInterfacialTension(ISpace) - Constructor for class etomica.data.DataProcessorInterfacialTension
DataProcessorInterfacialTensionProfile - Class in etomica.modules.interfacial
DataProcessorInterfacialTensionProfile(ISpace) - Constructor for class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
DataProcessorMu(AccumulatorHistory, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.DataProcessorMu
DataProcessorPhi - Class in etomica.densityofstate
DataProcessorPhi() - Constructor for class etomica.densityofstate.DataProcessorPhi
DataProcessorR2() - Constructor for class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
DataProcessorR2() - Constructor for class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
DataProcessorReweight - Class in etomica.liquidLJ: Takes incoming data, computes weight for configuration based on various cutoffs, multiplies each incoming data by the weight and also adds weights as extra data.
DataProcessorReweight(double, ValueCache, double[], IBox, int) - Constructor for class etomica.liquidLJ.DataProcessorReweight
DataProcessorReweight(double, LjMd3D.ValueCache, LjMd3D.ValueCache, double, double, double, IBox, IFunction) - Constructor for class etomica.liquidLJ.LjMd3D.DataProcessorReweight
DataProcessorReweightRatio - Class in etomica.liquidLJ: Takes incoming data sums including a weight sum for each cutoff, computes averages as sum/(weight sum)
DataProcessorReweightRatio(int) - Constructor for class etomica.liquidLJ.DataProcessorReweightRatio
DataProcessorReweightRatio(int, int) - Constructor for class etomica.liquidLJ.DataProcessorReweightRatio
DataProcessorSum - Class in etomica.normalmode: DataProcessor that sends on the sum of the incoming data values as a scalar.
DataProcessorSum() - Constructor for class etomica.normalmode.DataProcessorSum
DataProcessorSurfaceTension - Class in etomica.surfacetension
DataProcessorSurfaceTension() - Constructor for class etomica.surfacetension.DataProcessorSurfaceTension
DataProcessorTensorSplitter() - Constructor for class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
DataProcessorTensorSplitter() - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
DataProcessorTensorTrace() - Constructor for class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
DataProcessorVar - Class in etomica.modules.multiharmonic: Data Processor whose sole purpose in life is to discard the incoming data and push on the standard deviation from the accumulator.
DataProcessorVar() - Constructor for class etomica.modules.multiharmonic.DataProcessorVar
DataProcessorVirialOverlap - Class in etomica.virial.overlap: DataProcessor which takes in values for v/pi and pi2/pi (from MeterVirial) and calculates the overlap values for various values of alpha.
DataProcessorVirialOverlap(int, boolean) - Constructor for class etomica.virial.overlap.DataProcessorVirialOverlap
DataProcessorXY - Class in etomica.metastable
DataProcessorXY(DataDump) - Constructor for class etomica.metastable.DataProcessorXY
DataPump - Class in etomica.data: A DataProcessor whose action is to actively take Data from a DataSource and send it to DataSinks.
DataPump(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPump: Constructs DataPump with the given DataSource and DataSink.
dataPump - Variable in class etomica.graphics.DisplayTimer
dataPumpA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
DataPumpListener - Class in etomica.data
DataPumpListener(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListener
DataPumpListener(IEtomicaDataSource, IDataSink, int) - Constructor for class etomica.data.DataPumpListener
DataPumpListenerPow - Class in etomica.data: DataPump class that takes data at steps 2^i, i=0,1,2,3...
DataPumpListenerPow(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListenerPow
DataPumpListenerPow(IEtomicaDataSource, IDataSink, long, int, int) - Constructor for class etomica.data.DataPumpListenerPow
DataPumpListenerPowStrict - Class in etomica.data: DataPump class that takes data at steps pow^i, i=0,1,2,3...
DataPumpListenerPowStrict(IEtomicaDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListenerPowStrict
DataPumpListenerPowStrict(IEtomicaDataSource, IDataSink, int) - Constructor for class etomica.data.DataPumpListenerPowStrict
DataPumpListenerSmart - Class in etomica.data: Works with an instance of HistoryCollapsingDiscard to only retrieve new data from the datasource when the history will actually use the data.
DataPumpListenerSmart(IEtomicaDataSource, IDataSink, HistoryCollapsingDiscard) - Constructor for class etomica.data.DataPumpListenerSmart
DataPumpListenerSmart(IEtomicaDataSource, IDataSink, int, HistoryCollapsingDiscard) - Constructor for class etomica.data.DataPumpListenerSmart
dataPumps - Variable in class etomica.data.DataTableAverages
dataPumps - Variable in class etomica.thermointegration.IntegratorThermodynamic
dataseparator - Static variable in class org.jmol.script.Token
DataSet - Class in etomica.data: Receives and organizes data from multiple streams.
DataSet() - Constructor for class etomica.data.DataSet
DataSet(DataSet.DataCasterJudge) - Constructor for class etomica.data.DataSet
dataSet - Variable in class etomica.graphics.DisplayPlot
DataSet.DataCasterJudge - Interface in etomica.data
DataSet.DataSetSink - Class in etomica.data: A special DataSink used by the DataSet to receive Data and DataInfo from a single stream.
DataSetListener - Interface in etomica.data: Interface for a class that performs some action in response to a change in a DataSet instance.
DataSetSink(DataSet.DataCasterJudge, DataSet) - Constructor for class etomica.data.DataSet.DataSetSink
dataSink - Variable in class etomica.data.DataProcessor
dataSink - Variable in class etomica.virial.simulations.SimulationVirial
DataSinkConsole - Class in etomica.data: Writes data to console or another print stream.
DataSinkConsole() - Constructor for class etomica.data.DataSinkConsole: Makes class using System.out as the default output stream.
DataSinkConsole(PrintStream) - Constructor for class etomica.data.DataSinkConsole: Constructor that permits specification of the output printstream.
DataSinkExcludeOverlap(IBox) - Constructor for class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap(IBox) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap(Box) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
DataSinkExcludeOverlap() - Constructor for class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
dataSinkFactory - Variable in class etomica.data.DataDistributer
dataSinkFactory - Variable in class etomica.data.DataSplitter
dataSinkList - Variable in class etomica.data.DataFork
DataSinkReweightedDeltaU(AlphaSource) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
dataSinks - Variable in class etomica.data.DataDistributer
dataSinks - Variable in class etomica.data.DataGroupSplitter
dataSinks - Variable in class etomica.data.DataSplitter
DataSinkTable - Class in etomica.data: Receives data from multiple streams and organizes it in the form of a table, with each stream of data forming a column of the table.
DataSinkTable() - Constructor for class etomica.data.DataSinkTable
DataSinkTable.DataCasterJudgeTable - Class in etomica.data
dataSource - Variable in class etomica.data.DataPump
dataSourceA - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
DataSourceAcceptanceProbability - Class in etomica.data: Data source giving the average acceptance probability of MCMove type moves.
DataSourceAcceptanceProbability() - Constructor for class etomica.data.DataSourceAcceptanceProbability: Constructs with no MCMove specified.
DataSourceAcceptanceProbability(MCMove) - Constructor for class etomica.data.DataSourceAcceptanceProbability
DataSourceAcceptanceRatio - Class in etomica.data: Data source giving the acceptance rate of MCMove type moves.
DataSourceAcceptanceRatio() - Constructor for class etomica.data.DataSourceAcceptanceRatio: Constructs with no MCMove specified.
DataSourceAcceptanceRatio(MCMove) - Constructor for class etomica.data.DataSourceAcceptanceRatio
DataSourceAlphaAlpha(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
DataSourceAlphaAlpha(DataSourceVirialOverlap) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
DataSourceAlphaChi(MeterMBAR, MeterMBAR, boolean) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
DataSourceAlphaChi(DataOverlap, double) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
DataSourceAlphaChi(DataSourceVirialOverlap, double) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
DataSourceAlphaFE(AlphaSource, int) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
DataSourceAtomDistance - Class in etomica.data
DataSourceAtomDistance(ISpace) - Constructor for class etomica.data.DataSourceAtomDistance
DataSourceAtomic - Interface in etomica.data: Interface for a DataSource that can return a value given an arbitrary atom.
DataSourceAvgPressure - Class in etomica.normalmode: Averages the measured pressures for various N.
DataSourceAvgPressure(DataDistributer, MCMoveOverlapListener, double) - Constructor for class etomica.normalmode.DataSourceAvgPressure
DataSourceAvgPressure2 - Class in etomica.normalmode: Computes pressure from the grand canonical route based on measured free energy differences and simulation parameters.
DataSourceAvgPressure2(DataDistributer, MCMoveOverlapListener, double, double) - Constructor for class etomica.normalmode.DataSourceAvgPressure2
dataSourceB - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
DataSourceBias(AlphaSource) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
DataSourceChiSlope(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
DataSourceCollisional - Interface in etomica.data.meter: Interface for a meter that can return a value based on a hard-potential collision.
DataSourceCount() - Constructor for class etomica.data.AccumulatorHistory.DataSourceCount
DataSourceCountCollisions - Class in etomica.data: This is a data source to count the number of collisions processed by a hard-potential integrator.
DataSourceCountCollisions() - Constructor for class etomica.data.DataSourceCountCollisions: Sets up data source with no integrator specified.
DataSourceCountCollisions(IntegratorHard) - Constructor for class etomica.data.DataSourceCountCollisions
DataSourceCountSteps - Class in etomica.data: Data source that fronts the Integrator's step count as a piece of Data.
DataSourceCountSteps() - Constructor for class etomica.data.DataSourceCountSteps: Sets up data source to count integrator steps.
DataSourceCountSteps(IIntegrator) - Constructor for class etomica.data.DataSourceCountSteps
DataSourceCountTime - Class in etomica.data: Data source that keeps track of the elapsed simulation time of an MD integrator.
DataSourceCountTime() - Constructor for class etomica.data.DataSourceCountTime: Sets up data source with no integrator specified.
DataSourceCountTime(IntegratorMD) - Constructor for class etomica.data.DataSourceCountTime
DataSourceDensityFunction - Class in etomica.modules.adsorption
DataSourceDensityFunction(EOSSW, double, double) - Constructor for class etomica.modules.adsorption.DataSourceDensityFunction
DataSourceDensityFunction(EOSSW, double, double, boolean) - Constructor for class etomica.modules.adsorption.DataSourceDensityFunction
DataSourceEnergies - Class in etomica.freeenergy.npath: Created by andrew on 4/12/17.
DataSourceEnergies(PotentialMaster) - Constructor for class etomica.freeenergy.npath.DataSourceEnergies
DataSourceEnergies.PotentialCalculationEnergies - Class in etomica.freeenergy.npath
DataSourceExp(DataSourceUniform) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
DataSourceFE(String, MeterMBAR, MeterMBAR, int) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
DataSourceFE - Class in etomica.normalmode: Free energy data source that computes free energy differences based on overlap sampling performed by an MCMoveOverlapListener.
DataSourceFE(MCMoveOverlapListener) - Constructor for class etomica.normalmode.DataSourceFE
DataSourceFEHistogram - Class in etomica.normalmode: Returns a histogram of # of atoms based on free energy results and the given chemical potential.
DataSourceFEHistogram(MCMoveOverlapListener, double) - Constructor for class etomica.normalmode.DataSourceFEHistogram
DataSourceFunction - Class in etomica.data: Datasource formed as a wrapper around a function.
DataSourceFunction() - Constructor for class etomica.data.DataSourceFunction
DataSourceFunction(IFunction) - Constructor for class etomica.data.DataSourceFunction
DataSourceFunction(String, Dimension, IFunction, int) - Constructor for class etomica.data.DataSourceFunction
DataSourceFunction(String, Dimension, IFunction, int, String, Dimension) - Constructor for class etomica.data.DataSourceFunction
DataSourceFunctionRaw(double[], double[]) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
DataSourceGroup - Class in etomica.data: Collects one or more data sources into a single DataSource.
DataSourceGroup() - Constructor for class etomica.data.DataSourceGroup: Forms a DataSourceGroup that contains no data sources, and which will give an empty DataGroup for getData.
DataSourceGroup(IEtomicaDataSource[]) - Constructor for class etomica.data.DataSourceGroup: Forms a DataGroup containing the given data sources.
DataSourceImposedFEFit - Class in etomica.normalmode: Like DataSourceFEHistogram, returns a probability histogram for N based on free energies.
DataSourceImposedFEFit(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) - Constructor for class etomica.normalmode.DataSourceImposedFEFit
DataSourceImposedFEHistogram - Class in etomica.normalmode: This is a strange creature...
DataSourceImposedFEHistogram(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) - Constructor for class etomica.normalmode.DataSourceImposedFEHistogram
DataSourceIndependent - Interface in etomica.data: Interface for an object that can provide X Data objects on request.
DataSourceIndependentSimple - Class in etomica.data: A simple implementation of DataSourceIndependent objects can use if they cannot act as the DataSourceIndependent themselves (if perhaps they make multiple DataFunctions)
DataSourceIndependentSimple(double[], DataDoubleArray.DataInfoDoubleArray) - Constructor for class etomica.data.DataSourceIndependentSimple
DataSourceIndependentSimple(double[][], DataDoubleArray.DataInfoDoubleArray[]) - Constructor for class etomica.data.DataSourceIndependentSimple
dataSourceInfo - Variable in class etomica.data.DataPump
DataSourceMolecular - Interface in etomica.data: Interface for a DataSource that can return a value given an arbitrary atom.
DataSourceMuRoot - Class in etomica.normalmode: Datasource that returns an estimate of mu based on thermodynamic self-consistency of pressure measurements and defect free energies.
DataSourceMuRoot(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRoot
DataSourceMuRoot.DataSourceMuRootPressure - Class in etomica.normalmode
DataSourceMuRoot.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
DataSourceMuRoot1 - Class in etomica.normalmode: Datasource that returns an estimate of mu based on thermodynamic self-consistency of pressure measurements and defect free energies.
DataSourceMuRoot1(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRoot1
DataSourceMuRoot1.DataSourceMuRootPressure - Class in etomica.normalmode
DataSourceMuRoot1.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
DataSourceMuRootPMatch - Class in etomica.normalmode: Datasource that returns an estimate of mu based on thermodynamic self-consistency of pressure measurements and defect free energies.
DataSourceMuRootPMatch(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRootPMatch
DataSourceMuRootPMatch.DataSourceMuRootPressure - Class in etomica.normalmode
DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootPressure
DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootPressure
DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootPressure
DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration
DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
DataSourceOverlapAvgCollapsing() - Constructor for class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
DataSourceOverlapAvgCollapsingSplit(DataSplitter) - Constructor for class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
DataSourceOverlapAvgSimple(AccumulatorAverage) - Constructor for class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
DataSourcePMu - Class in etomica.normalmode: DataSource that returns P2-P1 or mu-mu* as a function of mu.
DataSourcePMu(MCMoveOverlapListener, double, int, double, DataDistributer, double, double, double, boolean) - Constructor for class etomica.normalmode.DataSourcePMu
DataSourcePN - Class in etomica.normalmode: DataSource that returns measured pressure as a function of N
DataSourcePN(DataDistributer, int) - Constructor for class etomica.normalmode.DataSourcePN
DataSourcePoints - Class in etomica.data
DataSourcePoints(String, Dimension, Dimension) - Constructor for class etomica.data.DataSourcePoints
DataSourcePositioned - Interface in etomica.data: Interface for a DataSource that can return a value given an arbitrary position.
DataSourcePositionedBoltzmannFactor - Class in etomica.data: Calculates the Boltzmann factor at a position within a box a molecule of a particular species would have if it existed at that point.
DataSourcePositionedBoltzmannFactor(ISpace) - Constructor for class etomica.data.DataSourcePositionedBoltzmannFactor
DataSourceProbabilityDensity - Class in etomica.modules.entropylottery
DataSourceProbabilityDensity() - Constructor for class etomica.modules.entropylottery.DataSourceProbabilityDensity
dataSourceRef - Variable in class etomica.overlap.MeterOverlap
dataSourceRefBias - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
dataSourceRefFE - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
dataSourceRefStdev - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
DataSourceRmsVelocity - Class in etomica.data: Meter for the root-mean-square velocity of a set of atoms.
DataSourceRmsVelocity() - Constructor for class etomica.data.DataSourceRmsVelocity
DataSourceRmsVelocity(Histogram) - Constructor for class etomica.data.DataSourceRmsVelocity
DataSourceScalar - Class in etomica.data: Particular data source for which the data is a simple scalar of type double.
DataSourceScalar(String, Dimension) - Constructor for class etomica.data.DataSourceScalar
dataSourceTarget - Variable in class etomica.overlap.MeterOverlap
dataSourceTargetBias - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
dataSourceTargetFE - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
dataSourceTargetStdev - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
DataSourceTensorVirialHard - Class in etomica.data: A MeterTensor that returns the virial component of the pressure tensor for a hard potential.
DataSourceTensorVirialHard(ISpace) - Constructor for class etomica.data.DataSourceTensorVirialHard
DataSourceTensorVirialHard(ISpace, IntegratorHard) - Constructor for class etomica.data.DataSourceTensorVirialHard
DataSourceTensorVirialHardProfile - Class in etomica.modules.interfacial: A DataSource that collects the average virial tensor as a function of position for one dimension.
DataSourceTensorVirialHardProfile(ISpace) - Constructor for class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
DataSourceTensorVirialHardProfile.DataSourceVirialProfile - Class in etomica.modules.interfacial
DataSourceUa(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
DataSourceUa2(IntegratorOverlap, DataOverlap, AccumulatorAverage, AccumulatorAverage) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
DataSourceUniform - Class in etomica.data: A DataSource object that provides a set of uniformly spaced values between two limits.
DataSourceUniform() - Constructor for class etomica.data.DataSourceUniform: Default constructor.
DataSourceUniform(String, Dimension) - Constructor for class etomica.data.DataSourceUniform
DataSourceUniform(String, Dimension, int, double, double) - Constructor for class etomica.data.DataSourceUniform: Constructs a DataSourceUniform using the indicated number of values and x range, and INCLUSIVE limits.
DataSourceUniform(String, Dimension, int, double, double, DataSourceUniform.LimitType, DataSourceUniform.LimitType) - Constructor for class etomica.data.DataSourceUniform: Constructs a DataSourceUniform using the indicated number of values, x range, and limit types, with dataInfo indicating that the data have the given dimension.
DataSourceUniform.LimitType - Class in etomica.data: Typed constant that indicates the way limits of the range are interpreted.
DataSourceVaporDensity(String, Dimension) - Constructor for class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
DataSourceVirialOverlap - Class in etomica.virial.overlap: Measures ratio of two cluster integrals using overlap sampling.
DataSourceVirialOverlap(AccumulatorVirialOverlapSingleAverage, AccumulatorVirialOverlapSingleAverage) - Constructor for class etomica.virial.overlap.DataSourceVirialOverlap
DataSourceVirialProfile(DataSourceTensorVirialHardProfile) - Constructor for class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
DataSourceWallPressure - Class in etomica.modules.pistoncylinder: data source front for virial sum from P1HardMovingBoundary returns pressure exerted on the wall by atoms
DataSourceWallPressure(ISpace, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.DataSourceWallPressure
DataSourceWallPressureCatalysis - Class in etomica.modules.catalysis
DataSourceWallPressureCatalysis(ISpace, ISpecies, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.DataSourceWallPressureCatalysis
DataSourceWallPressureMu - Class in etomica.modules.mu
DataSourceWallPressureMu(ISpace) - Constructor for class etomica.modules.mu.DataSourceWallPressureMu
DataSplitter - Class in etomica.data: DataSink that takes a Data object and pushes each numerical value from the incoming Data to a different stream.
DataSplitter() - Constructor for class etomica.data.DataSplitter
DataSplitter.IDataSinkFactory - Interface in etomica.data
DataStreamAction - Class in etomica.data
DataStreamAction() - Constructor for class etomica.data.DataStreamAction
DataStreamHeader - Class in etomica.simulation
DataTable - Class in etomica.data.types: Data object that holds double[] arrays as if they are columns in a table.
DataTable(int, int) - Constructor for class etomica.data.types.DataTable: Creates a new table with a specified number of columns all of a given length.
DataTable(DataDoubleArray[]) - Constructor for class etomica.data.types.DataTable
dataTable - Variable in class etomica.graphics.DisplayTable
DataTable.DataInfoTable - Class in etomica.data.types
DataTable.DataInfoTableFactory - Class in etomica.data.types
DataTableAverages - Class in etomica.data: Convenience class for a data table that collects the AccumulatorAverage statistics for a collection of DataSource instances.
DataTableAverages(IIntegrator) - Constructor for class etomica.data.DataTableAverages: Sets up table with default types that give the current value, the average, and the error bars.
DataTableAverages(IIntegrator, int, ArrayList<DataPump>) - Constructor for class etomica.data.DataTableAverages
DataTableAverages(IIntegrator, AccumulatorAverage.StatType[], int, IEtomicaDataSource[], ArrayList<DataPump>) - Constructor for class etomica.data.DataTableAverages: Sets up table with no sources.
DataTableListener - Interface in etomica.data: Interface for a class that performs some action in response to a change in a DataSinkTable instance.
DataTableWriter - Class in etomica.data: A DataWriter that writes out data as a table with optional column headings
DataTableWriter() - Constructor for class etomica.data.DataTableWriter
DataTag - Class in etomica.data: Class whose sole purpose is to implement Serializable so that data tags are serializable
DataTag() - Constructor for class etomica.data.DataTag
DataTagBag - Class in etomica.graphics: Simple class that associates a set of tags with an object (unit, label, etc)
DataTagBag(DataTag[], Object) - Constructor for class etomica.graphics.DataTagBag
DataTensor - Class in etomica.data.types: Data object wrapping a single mutable value of type (Space) Tensor.
DataTensor(ISpace) - Constructor for class etomica.data.types.DataTensor: Constructs a new instance with the given DataInfo, wrapping a new Tensor instance from the given space.
DataTensor.DataInfoTensor - Class in etomica.data.types
DataTensor.DataInfoTensorFactory - Class in etomica.data.types
dataTrueEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
dataVar - Variable in class etomica.modules.multiharmonic.DataProcessorVar
DataVector - Class in etomica.data.types: Data object wrapping a single mutable value of type (Space) Vector.
DataVector(ISpace) - Constructor for class etomica.data.types.DataVector: Constructs a new instance with the given DataInfo, wrapping a new Vector instance from the given space.
DataVector.DataInfoVector - Class in etomica.data.types
DataVector.DataInfoVectorFactory - Class in etomica.data.types
DataVirialOverlap - Class in etomica.virial.overlap: Convenience class that analyzes data from the reference and target system, providing average and error estimates on values and ratios.
DataVirialOverlap(AlphaSource, AccumulatorRatioAverageCovarianceFull, AccumulatorRatioAverageCovarianceFull) - Constructor for class etomica.virial.overlap.DataVirialOverlap
DataVirialOverlap.FullResult - Class in etomica.virial.overlap
dataWalkerAction(Object) - Method in class etomica.action.ResetAccumulators
dataWalkerAction(Object) - Method in class etomica.action.ResetAccumulatorsAveraged
dataWalkerAction(Object) - Method in class etomica.data.DataStreamAction
DataWriter(int, DisplayPlot) - Constructor for class etomica.graphics.DisplayPlot.DataWriter
dataWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
date - Static variable in class org.jmol.viewer.JmolConstants
dbc - Variable in class etomica.dimer.P1LepsHarmonic
DBDEN - Static variable in class etomica.math.Gamma
DBNUM - Static variable in class etomica.math.Gamma
DBO2C2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
DBO2H1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
dBOType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
DC - Static variable in class etomica.math.Gamma
dc11 - Variable in class etomica.normalmode.MeterSolidPropsLJ
DCF - Class in etomica.virial.cluster: Main method that simply generates and displays the graphs in the direct correlation function.
DCF() - Constructor for class etomica.virial.cluster.DCF
dcom - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
DCVGCMD - Class in etomica.modules.dcvgcmd: Dual-control-volume grand-canonical molecular dynamics simulation.
DCVGCMD() - Constructor for class etomica.modules.dcvgcmd.DCVGCMD
DCVGCMDGraphic - Class in etomica.modules.dcvgcmd
DCVGCMDGraphic(DCVGCMD, ISpace) - Constructor for class etomica.modules.dcvgcmd.DCVGCMDGraphic
DCVGCMDGraphic.Applet - Class in etomica.modules.dcvgcmd
dd(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
dd(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
dd - Variable in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
dd - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
dda - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
ddamp(int, double, double) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
dDimension() - Method in class etomica.units.DimensionRatio
ddP - Variable in class etomica.normalmode.MeterSolidProps
ddP - Variable in class etomica.normalmode.MeterSolidPropsLJ
DE(IVector) - Method in interface etomica.api.IVectorMutable: Divide-equals (/=) operation.
DE(IData) - Method in interface etomica.data.IData: Divide-equals (/=) operation.
DE(double) - Method in interface etomica.data.IData: Divide-equals (*=) operation, dividing all values in data by given value.
DE(IData) - Method in class etomica.data.types.DataDouble: Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataDouble: Divide-equals (/=) operation.
DE(IData) - Method in class etomica.data.types.DataDoubleArray: Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataDoubleArray: Divide-equals (*=) operation.
DE(IData) - Method in class etomica.data.types.DataDoubleBDArray: Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataDoubleBDArray: Times-equals (*=) operation.
DE(IData) - Method in class etomica.data.types.DataGroup
DE(double) - Method in class etomica.data.types.DataGroup
DE(IData) - Method in class etomica.data.types.DataTensor: Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataTensor: Divide-equals (*=) operation.
DE(IData) - Method in class etomica.data.types.DataVector: Divide-equals (/=) operation.
DE(double) - Method in class etomica.data.types.DataVector: Divide-equals (*=) operation.
DE(Tensor) - Method in interface etomica.space.Tensor
DE(Tensor) - Method in class etomica.space1d.Tensor1D
DE(IVector) - Method in class etomica.space1d.Vector1D
DE(Tensor) - Method in class etomica.space2d.Tensor2D
DE(IVector) - Method in class etomica.space2d.Vector2D
DE(Tensor) - Method in class etomica.space3d.Tensor3D
DE(IVector) - Method in class etomica.space3d.Vector3D
DE(Tensor) - Method in class etomica.spaceNd.TensorND
DE(IVector) - Method in class etomica.spaceNd.VectorND
DE(IBigValue) - Method in class etomica.veos.BigValue: Divide-equals (/=) operation.
DE(IBigValue) - Method in interface etomica.veos.IBigValue: Divide-equals (/=) operation.
DE(IBigValue) - Method in class etomica.veos.MyBigDecimal: Divide-equals (/=) operation.
deactivate() - Method in class etomica.util.Grabber.ActionCornerSetter
debug - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
debug - Variable in class etomica.models.co2.P2CO2Hellmann
debug - Static variable in class etomica.models.water.P2WaterSzalewicz
debug - Static variable in class etomica.potential.PotentialCalculationEnergySum
Debug - Class in etomica.util: Class holding static fields that determine whether debugging is on, how much, what types and what (if anything) should be looked at specifically.
Debug() - Constructor for class etomica.util.Debug
debug - Static variable in class etomica.virial.ClusterSum
debug - Static variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
debug - Variable in class etomica.virial.ClusterWheatleySoft
debug - Static variable in class etomica.virial.MayerGeneral
debug - Static variable in class org.jmol.script.Token
debug(String) - Method in class org.jmol.util.DefaultLogger
debug(String) - Static method in class org.jmol.util.Logger: Writes a log at DEBUG level.
debug(String) - Method in interface org.jmol.util.LoggerInterface: Writes a log at DEBUG level.
DEBUG_MODE - Static variable in class etomica.graph.engine.impl.ParserImpl
DEBUG_MODE - Static variable in class etomica.graph.iterators.filters.IsomorphismFilter
DEBUG_NOW - Static variable in class etomica.util.Debug: true if debugging is currently enabled (when the integrator reaches step START)
debugging - Variable in class etomica.models.co2.P2CO2H2OWheatley
debugging - Static variable in class org.jmol.util.Logger
debuggingHigh - Static variable in class org.jmol.util.Logger
debugme - Static variable in class etomica.models.co2.PNCO2GCPM
debugme - Static variable in class etomica.models.co2.PNGCPM
debugMoleculePair - Static variable in class etomica.util.Debug
debugPair - Static variable in class etomica.util.Debug
debugscript - Static variable in class org.jmol.script.Token
Debye - Class in etomica.units: The debye unit of electrical dipole moment, equal to 10^-18 statC-cm, or 3.33564e-30 C-m.
dec() - Method in interface etomica.graph.model.Bitmap: Decrements the integer value of this bitmap by one: bitmap--.
dec() - Method in class etomica.graph.model.impl.AbstractBitmap
decapitalize(String) - Static method in class etomica.util.Strings: Converts the first letter of the given string to lower case.
DECI - Static variable in class etomica.units.Prefix: Prefix indicating 10^-1 = 0.1.
Decimal - Class in etomica.units: Decimal representation of something that represents the fractional amount of a whole (e.g., mole fraction) as a decimal value typically between 0 and 1.
decimal - Static variable in class org.jmol.script.Token
DecimalSlider - Class in etomica.graphics: Slider that permits variation of decimal (non-integer) values.
DecimalSlider() - Constructor for class etomica.graphics.DecimalSlider
Decorate - Class in etomica.graph.operations: Performs decoration of diagrams by points.
Decorate() - Constructor for class etomica.graph.operations.Decorate
Decorate.DecorateParameters - Class in etomica.graph.operations
DecorateNaphthalene2Site(MulFlexible.MulFlexibleParameters, char, char, char, char, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
DecorateParameters(char, MulFlexible.MulFlexibleParameters) - Constructor for class etomica.graph.operations.Decorate.DecorateParameters
DecorateParameters(int, MulFlexible.MulFlexibleParameters) - Constructor for class etomica.graph.operations.Decorate.DecorateParameters
DecorateWertheim2Site - Class in etomica.graph.operations: Performs decoration of diagrams by various density points.
DecorateWertheim2Site() - Constructor for class etomica.graph.operations.DecorateWertheim2Site
DecorateWertheim2Site.DecorateWertheimParameters2Site - Class in etomica.graph.operations
DecorateWertheim2SiteRho - Class in etomica.graph.operations: Performs decoration of diagrams by various density points.
DecorateWertheim2SiteRho() - Constructor for class etomica.graph.operations.DecorateWertheim2SiteRho
DecorateWertheim2SiteRho.DecorateWertheimParameters2Site - Class in etomica.graph.operations
DecorateWertheim3SiteRho - Class in etomica.graph.operations: Performs decoration of diagrams by various density points.
DecorateWertheim3SiteRho() - Constructor for class etomica.graph.operations.DecorateWertheim3SiteRho
DecorateWertheim3SiteRho.DecorateWertheimParameters3Site - Class in etomica.graph.operations
DecorateWertheimNaphthalene2Rho - Class in etomica.graph.operations: modified from Hye Min's DecorateWertheim2SiteRho class Performs decoration of diagrams by various density points.
DecorateWertheimNaphthalene2Rho() - Constructor for class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site - Class in etomica.graph.operations
DecorateWertheimParameters2Site(int, MulFlexible.MulFlexibleParameters, char, char, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
DecorateWertheimParameters2Site(MulFlexible.MulFlexibleParameters, char, char, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
DecorateWertheimParameters3Site(MulFlexible.MulFlexibleParameters, char, char, char, char, char, char, char, char, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
decrementCollisionTime(double) - Method in class etomica.integrator.IntegratorHard.Agent: Decreases the recorded time to collision of this atom This action is performed when the atom is advanced without a collision
def - Variable in class etomica.modules.droplet.EllipseDisplayAction
DEF_ISOMORPHISM_ALGO - Static variable in class etomica.graph.isomorphism.Match
DEFAULT_ATOM_COLOR - Static variable in class etomica.graphics.ColorScheme
DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_HEIGHT - Static variable in class etomica.graph.view.rasterizer.SVGConverter: Default height
DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_INIT_SIZE - Static variable in class etomica.atom.AtomArrayList
DEFAULT_INIT_SIZE - Static variable in class etomica.atom.MoleculeArrayList
DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_MAX_TEMPERATURE - Static variable in class etomica.graphics.DeviceThermoSlider
DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_MIN_TEMPERATURE - Static variable in class etomica.graphics.DeviceThermoSlider
DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_QUALITY - Static variable in class etomica.graph.view.rasterizer.SVGConverter: Default quality value.
DEFAULT_RESULT_TYPE - Static variable in class etomica.graph.view.rasterizer.SVGConverter: Default result type
DEFAULT_SIZE - Static variable in class etomica.modules.crystalviewer.LatticeEditor
DEFAULT_STEREO_DEGREES - Static variable in enum org.jmol.constant.EnumStereoMode
DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
DEFAULT_WIDTH - Static variable in class etomica.graph.view.rasterizer.SVGConverter: Default width
defaultAdjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
defaultAdjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
defaultanglelabel - Static variable in class org.jmol.script.Token
defaultColor - Variable in class etomica.graphics.ColorScheme
defaultcolorscheme - Static variable in class org.jmol.script.Token
defaultColorsUsed - Variable in class etomica.graphics.ColorSchemeByType
defaultdirectory - Static variable in class org.jmol.script.Token
defaultdistancelabel - Static variable in class org.jmol.script.Token
defaultdrawarrowscale - Static variable in class org.jmol.script.Token
defaultdropscript - Static variable in class org.jmol.script.Token
defaultFileName() - Method in class etomica.data.DataLogger
defaultFontFamily - Variable in class etomica.graph.view.rasterizer.SVGConverter: Default value for the font-family when it is unspecified
defaultIOUnit() - Method in class etomica.data.DataSourceAcceptanceProbability
defaultIOUnit() - Method in class etomica.data.DataSourceAcceptanceRatio
DefaultIterator - Class in etomica.graph.iterators
DefaultIterator(byte) - Constructor for class etomica.graph.iterators.DefaultIterator
DefaultIterator(byte, byte) - Constructor for class etomica.graph.iterators.DefaultIterator
defaultlabelpdb - Static variable in class org.jmol.script.Token
defaultlabelxyz - Static variable in class org.jmol.script.Token
defaultlattice - Static variable in class org.jmol.script.Token
defaultloadfilter - Static variable in class org.jmol.script.Token
defaultloadscript - Static variable in class org.jmol.script.Token
DefaultLogger - Class in org.jmol.util: Default implementation of the logger.
DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
defaultMouseListener - Variable in class etomica.util.Grabber
DefaultMouseListener(Grabber) - Constructor for class etomica.util.Grabber.DefaultMouseListener
DefaultPermutator - Class in etomica.graph.iterators
DefaultPermutator(int[]) - Constructor for class etomica.graph.iterators.DefaultPermutator
defaults - Static variable in class org.jmol.script.Token
defaultstructuredssp - Static variable in class org.jmol.script.Token
DefaultSVGConverterController - Class in etomica.graph.view.rasterizer: Default controller for the SVGConverter operation.
DefaultSVGConverterController() - Constructor for class etomica.graph.view.rasterizer.DefaultSVGConverterController
DefaultToolbar - Class in etomica.graphics
DefaultToolbar() - Constructor for class etomica.graphics.DefaultToolbar
DefaultToolbar(JPanel, String) - Constructor for class etomica.graphics.DefaultToolbar
defaulttorsionlabel - Static variable in class org.jmol.script.Token
defaulttranslucent - Static variable in class org.jmol.script.Token
defaultValue() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
defaultvdw - Static variable in class org.jmol.script.Token
defBit(int, boolean) - Method in interface etomica.graph.model.Bitmap
defBit(int, boolean) - Method in class etomica.graph.model.impl.AbstractBitmap
defdfmt - Static variable in class etomica.util.ScientificFormat
defefmt - Static variable in class etomica.util.ScientificFormat
define - Static variable in class org.jmol.script.Token
deform(Tensor) - Method in class etomica.space.BoundaryDeformablePeriodic: Applies the given deformation tensor to the boundary in its current shape.
deformation - Variable in class etomica.modules.droplet.ConfigurationDroplet
Degree - Class in etomica.units: Standard degree angular unit, such that for example a right angle is 90 degrees.
degree() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Polynomial degree.
degree - Variable in class etomica.virial.MCMoveClusterAtomHSTree
degree - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
DEKA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺¹ = 10.
del_r - Variable in class etomica.virial.CalcFFT
delayExponent - Variable in class etomica.graphics.DeviceDelaySlider
delaymaximumms - Static variable in class org.jmol.script.Token
Delete - Class in etomica.graph.operations
Delete() - Constructor for class etomica.graph.operations.Delete
delete(int) - Method in class etomica.modules.render.ParseObj: Removes the vertex referenced by the given index from the list of vertices, removes its bonds from the list of bonds, shifts all vertex indexes down to fill its slot, and returns a list of indexes (after shifting) of vertices that were bonded to the given vertex.
delete - Static variable in class org.jmol.script.Token
deleteBits(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil: this one slides deleted bits out of a pattern.
deleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
deleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
deleteCandidateSet - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
deleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
deleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
deleteConnection(int, int) - Method in class etomica.virial.cluster.ClusterDiagram: Deletes a connection from one node1 to node2.
deleteEdge(byte) - Method in interface etomica.graph.model.Graph
deleteEdge(byte, byte) - Method in interface etomica.graph.model.Graph
deleteEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
deleteEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
DeleteEdge - Class in etomica.graph.operations: Deletes all edges of a given color.
DeleteEdge() - Constructor for class etomica.graph.operations.DeleteEdge
DeleteEdgeParameters - Class in etomica.graph.operations
DeleteEdgeParameters(char) - Constructor for class etomica.graph.operations.DeleteEdgeParameters
deleteElements(Object, int, int) - Static method in class org.jmol.util.ArrayUtil
deleteRow(int) - Method in class etomica.graphics.DeviceTableModelGeneric: Delete an entire row from the table
delta - Variable in class etomica.action.IntegratorDimerApproach
delta - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
delta1 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
delta1 - Variable in class etomica.normalmode.MCMoveSingleMode
delta2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
delta2 - Variable in class etomica.normalmode.MCMoveSingleMode
deltaA(double, double, int) - Method in class etomica.statmech.HardSphere: Returns the difference between absolute free energies between the given densities for solid (FCC) hard spheres.
deltaBMu - Variable in class etomica.normalmode.DataSourcePMu
deltaCut2 - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizable
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
deltaEps - Variable in class etomica.potential.P2PenetrableSquareWell
deltaMu - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
deltaP - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
deltaR - Variable in class etomica.dimer.IntegratorDimerMin
deltaR - Variable in class etomica.dimer.IntegratorDimerRT
deltaTheta - Variable in class etomica.dimer.IntegratorDimerMin
deltaTheta - Variable in class etomica.dimer.IntegratorDimerRT
deltaU - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
deltaU - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
deltaU - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
deltaU - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
deltaU - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
deltaU - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
deltaU - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
deltaU - Variable in class etomica.normalmode.MCMoveSingleMode
deltaV - Variable in class etomica.dimer.IntegratorDimerRT
deltaV - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
deltaX - Variable in class etomica.action.BoxInflateAnisotropic
deltaX - Variable in class etomica.util.HistogramNotSoSimple
deltaX - Variable in class etomica.util.HistogramReweightedData
deltaX - Variable in class etomica.util.HistogramSimple
deltaXl - Variable in class etomica.dimer.IntegratorDimerRT
deltaXmax - Variable in class etomica.dimer.IntegratorDimerRT
denom() - Method in class etomica.veos.bigdecimal.Rational: Get the denominator.
denominator - Variable in class etomica.util.Rational
denominator() - Method in class etomica.util.Rational: Returns the denominator.
denomSum - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
denomSum - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
denomSum - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
denomSum - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
denomSum - Variable in class etomica.normalmode.MeterWorkTargetBennet
denomSum - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
denomSum - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
denomSum - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
dense - Variable in class etomica.potential.P2QChemInterpolated
density - Variable in class etomica.AlkaneEH.CH4NVT.Param
density - Variable in class etomica.AlkaneEH.DHS_NVT.Param
density - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
density - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
density - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
density - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
density - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
density - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
density - Variable in class etomica.dielectric.DHS_NVT.Param
density - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
density - Variable in class etomica.dielectric.TIP4P_NVT.Param
density - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
density - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
density - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
density - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
density - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
density - Variable in class etomica.mappedvirial.MappedU.LJMDParams
density - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
density - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
density - Variable in class etomica.meam.EFSTungsten.Params
density - Variable in class etomica.metastable.LJNPT.LJMCParams
density - Variable in class etomica.metastable.LJNVT.LJMCParams
density - Variable in class etomica.models.nitrogen.FindTransitionTemperature
density - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
density - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
density - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
density - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
density - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
density - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
density - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
density - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
density - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
density - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
density - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
density - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
density - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
density - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
density - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
density - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
density - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
density - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
density - Variable in class etomica.modules.droplet.DropletAtomic
density - Variable in class etomica.modules.render.RenderMD.RenderMDParam
density - Variable in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
density - Variable in class etomica.modules.vle.MCMoveVolumeExchangeVLE
density - Variable in class etomica.modules.vle.VLESim
density - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
density - Variable in class etomica.normalmode.MeterSolidProps
density - Variable in class etomica.normalmode.MeterSolidPropsLJ
density - Variable in class etomica.normalmode.MinimizeHCP
density - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
density - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
density - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
density - Variable in class etomica.normalmode.SimBennet.SimBennetParam
density - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
density - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
density - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
density - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
density - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
density - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
density - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
density - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
density - Variable in class etomica.normalmode.SimLJVacancy.LJParams
density - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
density - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
density - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
density - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
density - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
density - Variable in class etomica.statmech.HardSphereSolid.EOSParams
density - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
density1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
density2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
densityAccum - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
densityBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
densityDisplay - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
densityDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
densityForMu(double) - Static method in class etomica.statmech.HardSphereSolid
densityForPressure(double) - Static method in class etomica.statmech.HardSphereSolid
densityMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
DensityOfState - Class in etomica.densityofstate: A Yukawa Monte-Carlo simulation in 3D
DensityOfState() - Constructor for class etomica.densityofstate.DensityOfState
DensityOfState(int) - Constructor for class etomica.densityofstate.DensityOfState
DensityOfStatesPolynomial - Class in etomica.densityofstate: A Yukawa Monte-Carlo simulation in 3D
DensityOfStatesPolynomial() - Constructor for class etomica.densityofstate.DensityOfStatesPolynomial
DensityOfStatesPolynomial(int) - Constructor for class etomica.densityofstate.DensityOfStatesPolynomial
densityProfileMeter - Variable in class etomica.modules.colloid.ColloidGraphic
densityProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
densityProfileMeter - Variable in class etomica.surfacetension.SurfaceTensionMapped
densityProfileMeterA - Variable in class etomica.modules.adsorption.AdsorptionGraphic
densityProfileMeterB - Variable in class etomica.modules.adsorption.AdsorptionGraphic
densityProfileSource - Variable in class etomica.data.DataProcessorChemicalPotential
depth - Static variable in class org.jmol.script.Token
depth - Variable in class org.jmol.util.GData
DepthFirst - Class in etomica.graph.traversal
DepthFirst() - Constructor for class etomica.graph.traversal.DepthFirst
depthValue - Variable in class g3dsys.control.TransformManager
derivative2nd(IVectorMutable, Potential2SoftSpherical) - Method in class etomica.normalmode.HessianDB
DerivativeEnergyFunction - Class in etomica.conjugategradient
DerivativeEnergyFunction(IBox, PotentialMaster, ISpace) - Constructor for class etomica.conjugategradient.DerivativeEnergyFunction
DerivativeEnergyFunction.MyAgentSource - Class in etomica.conjugategradient
derivativeFunction - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
derive() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: First derivative.
description() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
desiredPressure - Variable in class etomica.models.nitrogen.FindTransitionTemperature
dest - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
dest - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
dest - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
dest - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
destination - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
destination - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
DestinationType - Class in etomica.graph.view.rasterizer: Describes the type of destination for an SVGConverter operation.
destinationType - Variable in class etomica.graph.view.rasterizer.SVGConverter: Result type
destroy() - Method in class org.jmol.g3d.Graphics3D
destroy() - Method in class org.jmol.util.GData
det(BigInteger[][]) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Determinant of an integer square matrix.
determinant() - Method in interface etomica.space.Tensor
determinant() - Method in class etomica.space1d.Tensor1D
determinant() - Method in class etomica.space2d.Tensor2D
determinant() - Method in class etomica.space3d.Tensor3D
determinant() - Method in class etomica.spaceNd.TensorND
determinant() - Method in class org.jmol.util.Matrix3f: Computes the determinant of this matrix.
determinant() - Method in class org.jmol.util.Matrix4f: Computes the determinant of this matrix.
deviationVector - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
Device - Class in etomica.graphics: Base class for all Devices.
Device() - Constructor for class etomica.graphics.Device
Device(IController) - Constructor for class etomica.graphics.Device
Device.ActionSet - Class in etomica.graphics
DeviceBox - Class in etomica.graphics: A simple device the permits editing of a single value via a textbox with an associated label.
DeviceBox() - Constructor for class etomica.graphics.DeviceBox
DeviceBox.LabelType - Class in etomica.graphics: Typed constant used to indicate the type of label to be used with the display.
deviceBoxValueChanged(DeviceBoxValueChangedEvent) - Method in class etomica.graphics.DeviceBox
deviceBoxValueChanged(DeviceBoxValueChangedEvent) - Method in interface etomica.graphics.DeviceBoxValueChangedListener
DeviceBoxValueChangedEvent - Class in etomica.graphics
DeviceBoxValueChangedEvent(DeviceBox, int) - Constructor for class etomica.graphics.DeviceBoxValueChangedEvent
DeviceBoxValueChangedListener - Interface in etomica.graphics: Interface that should be implemented to receive a value changed event when a DeviceBox updateValue method is called.
DeviceButton - Class in etomica.graphics: Button that causes an action to be performed.
DeviceButton(IController) - Constructor for class etomica.graphics.DeviceButton: Constructs button that is not connected to any action.
DeviceButton(IController, IAction) - Constructor for class etomica.graphics.DeviceButton: Constructs a button connected to the given action.
DeviceButtonGroup - Class in etomica.graphics: Add etomica device for a group of radio buttons.
DeviceButtonGroup(IController, int) - Constructor for class etomica.graphics.DeviceButtonGroup
DeviceButtonSingle - Class in etomica.zeolite: Button that causes an action to be performed.
DeviceButtonSingle(IController) - Constructor for class etomica.zeolite.DeviceButtonSingle: Constructs button that is not connected to any action.
DeviceButtonSingle(IController, IAction) - Constructor for class etomica.zeolite.DeviceButtonSingle: Constructs a button connected to the given action.
DeviceCellNum3DSlider - Class in etomica.normalmode
DeviceCellNum3DSlider(IController) - Constructor for class etomica.normalmode.DeviceCellNum3DSlider
DeviceCellNumXYSlider - Class in etomica.normalmode
DeviceCellNumXYSlider(IController) - Constructor for class etomica.normalmode.DeviceCellNumXYSlider
DeviceCheckBox - Class in etomica.graphics: Button that toggles a boolean value via a check box.
DeviceCheckBox(ModifierBoolean) - Constructor for class etomica.graphics.DeviceCheckBox
DeviceCheckBox(String, ModifierBoolean) - Constructor for class etomica.graphics.DeviceCheckBox
DeviceControllerButton - Class in etomica.graphics: Button that attaches to a controller to toggle its pause/resume state.
DeviceControllerButton(Controller) - Constructor for class etomica.graphics.DeviceControllerButton
DeviceDelaySlider - Class in etomica.graphics
DeviceDelaySlider(IController, ActivityIntegrate) - Constructor for class etomica.graphics.DeviceDelaySlider
DeviceEigenvaluesSlider - Class in etomica.normalmode
DeviceEigenvaluesSlider(IController) - Constructor for class etomica.normalmode.DeviceEigenvaluesSlider
deviceList() - Method in class etomica.graphics.SimulationGraphic
DeviceNSelector - Class in etomica.graphics: Slider that selects the number of atoms of a given species in a box.
DeviceNSelector() - Constructor for class etomica.graphics.DeviceNSelector
DeviceNSelector(IController) - Constructor for class etomica.graphics.DeviceNSelector
DevicePlotPoints - Class in etomica.graphics
DevicePlotPoints(IFunction[], String[], String[]) - Constructor for class etomica.graphics.DevicePlotPoints
DevicePlotPoints(String[], IFunction[], String[], boolean) - Constructor for class etomica.graphics.DevicePlotPoints
DeviceSelector - Class in etomica.graphics: Generic Device that has a combo box.
DeviceSelector(IController) - Constructor for class etomica.graphics.DeviceSelector
DeviceSlider - Class in etomica.graphics: Device the changes a property using a graphical slider, via a Modifier.
DeviceSlider(IController) - Constructor for class etomica.graphics.DeviceSlider
DeviceSlider(IController, Object, String) - Constructor for class etomica.graphics.DeviceSlider: Constructs a slider connected to the given property of the given object
DeviceSlider(IController, Modifier) - Constructor for class etomica.graphics.DeviceSlider: Constructs a slider connected to the get/set Value methods of the given Modifier
DeviceSpinner - Class in etomica.graphics: Device the changes a property using a graphical spinner, via a Modifier.
DeviceSpinner(IController) - Constructor for class etomica.graphics.DeviceSpinner
DeviceSpinner(IController, Object, String) - Constructor for class etomica.graphics.DeviceSpinner: Constructs a spinner connected to the given property of the given object
DeviceSpinner(IController, Modifier) - Constructor for class etomica.graphics.DeviceSpinner: Constructs a spinner connected to the get/set Value methods of the given Modifier
DeviceSpinner.SpinnerListener - Class in etomica.graphics: Spinner listener, which relays the spinner change events to the modifier
DeviceTable - Class in etomica.graphics: Presents a table of numeric properties that can be edited by typing in values.
DeviceTable(String[]) - Constructor for class etomica.graphics.DeviceTable
DeviceTable(TableModel) - Constructor for class etomica.graphics.DeviceTable
DeviceTableModelGeneric - Class in etomica.graphics
DeviceTableModelGeneric(Object[][], String[]) - Constructor for class etomica.graphics.DeviceTableModelGeneric
DeviceTernarySelector - Class in etomica.graphics: Selector for fractions in a ternary system.
DeviceTernarySelector() - Constructor for class etomica.graphics.DeviceTernarySelector
DeviceTernarySelector(String[]) - Constructor for class etomica.graphics.DeviceTernarySelector: Creates a new devices using the given labels for the diagram.
DeviceTernarySelector.Listener - Interface in etomica.graphics
DeviceTernarySelector.MyEventManager - Class in etomica.graphics
DeviceThermoSelector - Class in etomica.graphics: Permits selection of temperature from a discrete set of values.
DeviceThermoSelector(Simulation, IntegratorBox) - Constructor for class etomica.graphics.DeviceThermoSelector: Constructor that specifies Kelvin as temperature units.
DeviceThermoSelector(IController, Unit, boolean) - Constructor for class etomica.graphics.DeviceThermoSelector
DeviceThermoSlider - Class in etomica.graphics
DeviceThermoSlider(IController, IntegratorBox) - Constructor for class etomica.graphics.DeviceThermoSlider
DeviceThermoSliderGEMC - Class in etomica.modules.vle: Custom temperature slider for GEMC simulations.
DeviceThermoSliderGEMC(IController) - Constructor for class etomica.modules.vle.DeviceThermoSliderGEMC
DeviceToggleButton - Class in etomica.graphics: Button that toggles a boolean value.
DeviceToggleButton(IController) - Constructor for class etomica.graphics.DeviceToggleButton
DeviceToggleButton(IController, ModifierBoolean) - Constructor for class etomica.graphics.DeviceToggleButton
DeviceToggleButton(IController, ModifierBoolean, String, String) - Constructor for class etomica.graphics.DeviceToggleButton
DeviceToggleRadioButtons - Class in etomica.graphics: Button that toggles a boolean value using a pair of radio buttons.
DeviceToggleRadioButtons(ModifierBoolean) - Constructor for class etomica.graphics.DeviceToggleRadioButtons: Constructor with default labels of a blank title and "True" and "False" for the true/false labels.
DeviceToggleRadioButtons(ModifierBoolean, String, String, String) - Constructor for class etomica.graphics.DeviceToggleRadioButtons
DeviceTrioControllerButton - Class in etomica.graphics: Device comprising three buttons: (1) attaches to a controller to toggle its pause/resume state; (2)causes a reset (restart) action of simulation to be performed; (3) causes reset of meter averages only.
DeviceTrioControllerButton(ISimulation, ISpace, Controller) - Constructor for class etomica.graphics.DeviceTrioControllerButton: Contructs device with buttons that affect the given simulation.
DeviceTrioControllerButton() - Constructor for class etomica.graphics.DeviceTrioControllerButton: No-argument contructor gives device that performs no action until setSimulation is used to specify the target simulation.
DeviceTrioControllerButton.ComponentEventControllerButton - Class in etomica.graphics: Inner class that catches action of simulation panel
DeviceWaveVectorSlider - Class in etomica.normalmode
DeviceWaveVectorSlider(IController) - Constructor for class etomica.normalmode.DeviceWaveVectorSlider
df(int[], double[]) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
df(int[], double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
df(int[], double[]) - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
df(int[], int, double[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
df(int[], double[]) - Method in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
df(int[], double[]) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
df(int, double) - Method in class etomica.util.Function.Abs
df(int, double) - Method in class etomica.util.Function.Constant
df(int, double) - Method in class etomica.util.Function.Exp
df(int, double) - Method in class etomica.util.Function.Identity
df(int, double) - Method in class etomica.util.Function.Linear
df(int, double) - Method in class etomica.util.Function.Log
df(int, double) - Method in class etomica.util.Function.Reciprocal
df(int, double) - Method in class etomica.util.Function.Sqrt
df(int, double) - Method in class etomica.util.FunctionChain: Evaluates derivative via the chain rule.
df(int, double) - Method in interface etomica.util.FunctionDifferentiable
df(int[], double[]) - Method in interface etomica.util.FunctionMultiDimensionalDifferentiable: Returns the derivative indicated by the array d evaluated at the given point x.
df(int[], double[]) - Method in class etomica.util.numerical.CalcGradientDifferentiable
df(int[], double[]) - Method in class etomica.util.numerical.FiniteDifferenceDerivative
df(int, double[], double) - Method in class etomica.util.numerical.FittingFunctionNonLinear
df(int, double[], double) - Method in class etomica.util.numerical.FittingFunctionNonLinearB
df(int, double) - Method in class etomica.util.numerical.Function1d
df2(int[], double[]) - Method in class etomica.util.numerical.CalcGradientDifferentiable: Uses the potential's force calculation at different displacements of a molecule in X, Y and Z to determine the second derivative of the potential.
dfdx(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
dfmt - Variable in class etomica.util.ScientificFormat
dForces - Variable in class etomica.dimer.SimDimerLJadatom
dForces - Variable in class etomica.dimer.SimDimerMEAMadatom
dForces - Variable in class etomica.dimer.SimDimerMEAMGB
dForces - Variable in class etomica.kmc.SimKMCMEAMadatom
dFrot - Variable in class etomica.dimer.IntegratorDimerMin
dFrot - Variable in class etomica.dimer.IntegratorDimerRT
dFsq - Variable in class etomica.dimer.IntegratorDimerRT
DHS_NVT - Class in etomica.AlkaneEH: Canonical ensemble Monte Carlo simulation (NVT) calculate dielectric constant for dipolar HS model
DHS_NVT(Space, int, double, double, double, double, double, double) - Constructor for class etomica.AlkaneEH.DHS_NVT
DHS_NVT - Class in etomica.dielectric: Canonical ensemble Monte Carlo simulation (NVT) calculate dielectric constant for dipolar HS model Electric field mapped average for dielectric constant
DHS_NVT(Space, int, double, double, double, double, double, double) - Constructor for class etomica.dielectric.DHS_NVT
DHS_NVT.DipoleSourceDHS - Class in etomica.AlkaneEH
DHS_NVT.DipoleSourceDHS - Class in etomica.dielectric
DHS_NVT.Param - Class in etomica.AlkaneEH
DHS_NVT.Param - Class in etomica.dielectric
dHSCore - Static variable in class etomica.potential.P2NitrogenHellmann
diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
diagramIndex - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
diagramIndex - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
DiagramSource - Interface in etomica.virial.cluster
diameter - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
DiameterHash - Interface in etomica.atom: This provides an interface for a class that acts like a hashmap for atomic diameters.
diameterHash - Variable in class etomica.graphics.DisplayBox
diameterHash - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
diameterHash - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
DiameterHashByElement - Class in etomica.atom: This class hashes atomic diameters based on the element.
DiameterHashByElement() - Constructor for class etomica.atom.DiameterHashByElement
DiameterHashByElementType - Class in etomica.atom: This class hashes atomic diameters based on both element and atom type.
DiameterHashByElementType(ISimulation) - Constructor for class etomica.atom.DiameterHashByElementType
DiameterHashByType - Class in etomica.atom: This class hashes atomic diameters based on the atom type.
DiameterHashByType(ISimulation) - Constructor for class etomica.atom.DiameterHashByType
diameterManagerByElement - Variable in class etomica.atom.DiameterHashByElementType
dielectricOutside - Variable in class etomica.AlkaneEH.DHS_NVT.Param
dielectricOutside - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
dielectricOutside - Variable in class etomica.dielectric.DHS_NVT.Param
dielectricOutside - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
dielectricOutside - Variable in class etomica.dielectric.TIP4P_NVT.Param
DifByConstant - Class in etomica.graph.operations
DifByConstant() - Constructor for class etomica.graph.operations.DifByConstant
DifByConstant.DifByConstantParameters - Class in etomica.graph.operations
DifByConstantParameters(char, char) - Constructor for class etomica.graph.operations.DifByConstant.DifByConstantParameters
DifByEdge - Class in etomica.graph.operations
DifByEdge() - Constructor for class etomica.graph.operations.DifByEdge
DifByNode - Class in etomica.graph.operations
DifByNode() - Constructor for class etomica.graph.operations.DifByNode
diff - Variable in class etomica.util.numerical.B9Optimizer
diff - Variable in class etomica.util.numerical.VirialOptimizer
diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
difference(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Generates the set of diagrams obtained by subtracting the second set from the first set.
diffuseFactor - Static variable in class org.jmol.util.Shader
diffusepercent - Static variable in class org.jmol.script.Token
diffusePercent - Static variable in class org.jmol.util.Shader
DifParameters - Class in etomica.graph.operations
DifParameters(char) - Constructor for class etomica.graph.operations.DifParameters
digits - Variable in class etomica.graphics.DisplayTable
dihedralAngle(Plane) - Method in class etomica.math.geometry.Plane: Dihedral angle between this plane and the given plane.
dim - Variable in class etomica.action.BoxQuench
dim - Variable in class etomica.lattice.IndexIteratorIncreasing
dim - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
dim - Variable in class etomica.modules.adsorption.MyMCMove
dim - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
dim - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
dim - Variable in class etomica.modules.rosmosis.MeterFlux
dim - Variable in class etomica.normalmode.MeterSolidDA
dim - Variable in class etomica.normalmode.MeterSolidDACut
dim - Variable in class etomica.spaceNd.TensorND
dimension - Variable in class etomica.data.DataInfoFactory
DIMENSION - Static variable in class etomica.units.Angle
DIMENSION - Static variable in class etomica.units.Area
DIMENSION - Static variable in class etomica.units.Charge: Singleton instance of this class.
dimension() - Method in class etomica.units.CompoundUnit
DIMENSION - Static variable in class etomica.units.Current: Singleton instance of this class.
Dimension - Class in etomica.units: Parent of all Dimension classes, which describe the physical dimensions (e.g., mass, length, force) of a quantity.
Dimension(String, double, double, double) - Constructor for class etomica.units.Dimension
Dimension(String, double, double, double, double, double, double, double) - Constructor for class etomica.units.Dimension
Dimension(String, double[]) - Constructor for class etomica.units.Dimension
DIMENSION - Static variable in class etomica.units.Dipole
DIMENSION - Static variable in class etomica.units.ElectricPotential: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Energy: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Force
DIMENSION - Static variable in class etomica.units.Fraction: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Length: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.LuminousIntensity: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Mass: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Null: Singleton instance of this class.
dimension() - Method in class etomica.units.PrefixedUnit: Returns the dimension of this baseUnit.
DIMENSION - Static variable in class etomica.units.Pressure: Singleton instance of this class.
dimension(int) - Static method in class etomica.units.Pressure: Returns the Dimension instance for the "pressure" appropriate to the given dimension.
DIMENSION - Static variable in class etomica.units.Pressure2D
DIMENSION - Static variable in class etomica.units.Quantity: Singleton instance of this class.
dimension() - Method in class etomica.units.SimpleUnit: Returns the dimension of this base unit.
dimension() - Method in class etomica.units.systems.LJ.LJUnit
DIMENSION - Static variable in class etomica.units.Temperature: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Time: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Undefined: Singleton instance of this class.
dimension() - Method in interface etomica.units.Unit: Returns the dimension of the unit.
DIMENSION - Static variable in class etomica.units.Viscosity: Singleton instance of this class.
DIMENSION - Static variable in class etomica.units.Volume: Singleton instance of this class.
dimension(int) - Static method in class etomica.units.Volume: Returns the Dimension instance for the "volume" appropriate to the given dimension.
Dimensioned - Interface in etomica.units: Interface for an object with an associated physical dimension.
DimensionedDoubleEditor - Class in etomica.graphics: Editor to set the value of a double-type property having units associated with it.
DimensionedDoubleEditor(Dimension) - Constructor for class etomica.graphics.DimensionedDoubleEditor
DimensionRatio - Class in etomica.units: Class to form a dimension from ratio of two dimensions.
DimensionRatio(Dimension, Dimension) - Constructor for class etomica.units.DimensionRatio
DimensionRatio(String, Dimension, Dimension) - Constructor for class etomica.units.DimensionRatio
dimensions() - Method in class etomica.graphics.DisplayPolytope: returns dimensions of polytope as the (max - min) value in each dimension for all the vertices.
dimensions - Variable in class etomica.space.BoundaryRectangular
dimensions - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
dimensionsHalf - Variable in class etomica.space.BoundaryRectangularPeriodic
dimensionsHalf - Variable in class etomica.space.BoundaryRectangularPore
dimensionsHalf - Variable in class etomica.space.BoundaryRectangularSlit
dimensionsHalf - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
dimensionString() - Static method in class etomica.units.Lister
dimer - Variable in class etomica.dimer.SimDimerMEAMGB
DimerApproach - Class in etomica.models.rowley
DimerApproach() - Constructor for class etomica.models.rowley.DimerApproach
dimerApproach - Variable in class etomica.models.rowley.DimerApproach
dimerAtomType - Variable in class etomica.normalmode.SpeciesHSDimer
dimerColorManager - Variable in class etomica.association.ColorSchemeSmer
dimerCurvature(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT: Computes curvature value, C, for the energy surface.
dimerForceCenter(IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
dimerForceEff(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
dimerForcePerp(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerMin: Finds the component of the dimer's total force that is perpendicular to the normal vector.
dimerForcePerp(IVectorRandom[], IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
dimerForces(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerMin: Resets forces in boxes 0 and min, calls potential.calculate, and copies over the new forces to local arrays.
dimerForces(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
dimerForcesStar(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerMin: Used in the middle of the rotateDimer method.
dimerForcesStar(IVectorMutable[], IVectorMutable[], IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
dimerNormal() - Method in class etomica.dimer.IntegratorDimerMin: Computes an n-dimensional vector in potential energy hyperspace, pointing in the direction of the dimer (intersecting both simulation boxes).
dimerNormal() - Method in class etomica.dimer.IntegratorDimerRT
dimerPotential - Variable in class etomica.association.MCMoveDimer
dimerPotential - Variable in class etomica.association.MCMoveDimerRotate
dimerPotential - Variable in class etomica.integrator.mcmove.MCMoveDimer
dimerPotential - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
dimerPump - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
dimerSaddleTolerance() - Method in class etomica.dimer.IntegratorDimerRT
dimerUpdatePositions(double, IVectorMutable[]) - Method in class etomica.dimer.IntegratorDimerRT
dimVector - Variable in class etomica.action.BoxInflate
dimx - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
dimy - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
dipind(int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
dipole - Variable in class etomica.dielectric.TIP4P_NVT.DipoleSourceTIP4PWater
dipole - Variable in class etomica.models.aceticAcid.DipoleSourceAceticAcid
dipole - Variable in class etomica.models.water.DipoleSourceWater
Dipole - Class in etomica.units: Base unit for electrical dipole moment.
dipole() - Method in class etomica.units.systems.CGS
dipole() - Method in class etomica.units.systems.LJ
dipole() - Method in class etomica.units.systems.MKS
dipole() - Method in class etomica.units.systems.UnitSystem
dipole() - Method in class etomica.units.systems.UnitSystem.Sim
dipole - Static variable in class org.jmol.script.Token
DipoleBox - Class in etomica.rotation
DipoleBox(ISpace, int, double) - Constructor for class etomica.rotation.DipoleBox
DipoleBox.Applet - Class in etomica.rotation
DipoleBoxMatrix - Class in etomica.rotation
DipoleBoxMatrix(ISpace, int, double) - Constructor for class etomica.rotation.DipoleBoxMatrix
DipoleBoxMatrix.Applet - Class in etomica.rotation
dipoleFShift - Variable in class etomica.rotation.P2LJDipole
dipolescale - Static variable in class org.jmol.script.Token
DipoleSource - Interface in etomica.atom: Interface for something that can calculate the dipole of a molecule.
dipoleSource - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
dipoleSource - Variable in class etomica.potential.P1ExternalField
dipoleSource - Variable in class etomica.potential.P2ReactionFieldDipole
dipoleSource - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
dipoleSource - Variable in class etomica.potential.PotentialCalculationPhiSum
DipoleSourceAceticAcid - Class in etomica.models.aceticAcid: dipole for acetic acid
DipoleSourceAceticAcid(ISpace) - Constructor for class etomica.models.aceticAcid.DipoleSourceAceticAcid
DipoleSourceDHS(ISpace, double) - Constructor for class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
DipoleSourceDHS(ISpace, double) - Constructor for class etomica.dielectric.DHS_NVT.DipoleSourceDHS
DipoleSourceDLJ(ISpace, double) - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
DipoleSourceDLJ(ISpace, double) - Constructor for class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
DipoleSourceTIP4PWater(ISpace) - Constructor for class etomica.dielectric.TIP4P_NVT.DipoleSourceTIP4PWater
DipoleSourceWater - Class in etomica.models.water: Implementation of DipoleSource that can handle water molecules that are MoleculeOriented.
DipoleSourceWater(ISpace) - Constructor for class etomica.models.water.DipoleSourceWater
dipoleStrength - Variable in class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
dipoleStrength - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
dipoleStrength - Variable in class etomica.dielectric.DHS_NVT.DipoleSourceDHS
dipoleStrength - Variable in class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
dipoleStrength - Variable in class etomica.models.water.DipoleSourceWater
dipoleStrength2 - Variable in class etomica.AlkaneEH.DHS_NVT.Param
dipoleStrength2 - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
dipoleStrength2 - Variable in class etomica.dielectric.DHS_NVT.Param
dipoleStrength2 - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
dipoleUShift - Variable in class etomica.rotation.P2LJDipole
dipoleVector - Variable in class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
dipoleVector - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
dipoleVector - Variable in class etomica.dielectric.DHS_NVT.DipoleSourceDHS
dipoleVector - Variable in class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
dir0 - Variable in class etomica.potential.P2SpheroPolyhedron
dir1 - Variable in class etomica.potential.P2SpheroPolyhedron
dir2 - Variable in class etomica.potential.P2SpheroPolyhedron
direction() - Method in class etomica.atom.iterator.IteratorDirective
direction - Variable in class etomica.atom.iterator.MpiIntraspecies1A
direction - Variable in class etomica.config.ConfigurationOrientedFile
direction - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
direction - Variable in class etomica.space2d.Orientation2D
direction - Variable in class etomica.space3d.Orientation3D
direction - Variable in class etomica.space3d.OrientationFull3D
DirectSamplingTargetQCArReferenceAzizAr - Class in etomica.virial.simulations: This class used the direct-sampling formulation of Mayer-Sampling Monte Carlo to compute the second virial coefficient of argon, as described with a quantum potential (via Q-Chem), at a particular temperature.
DirectSamplingTargetQCArReferenceAzizAr() - Constructor for class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr
DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
dirty - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
dirty - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
dirty - Variable in class etomica.util.numerical.AkimaSpline
DirtyObject - Interface in etomica.util
disablepopupmenu - Static variable in class org.jmol.script.Token
DiscardCriteria(char, int, char, int) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.DiscardCriteria
disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagrams
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsMix
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsMix2
disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsPT
disconnectedP - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
disconnectedP - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
disp - Variable in class etomica.potential.P2QChemInterpolated
disp - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
disp - Variable in class etomica.potential.P3QChem.DampingParams
displacementLimit2 - Variable in class etomica.nbr.CriterionSimple
displacementLimit2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
display(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
Display - Class in etomica.graphics: Superclass of all classes that display something from the simulation.
Display() - Constructor for class etomica.graphics.Display
display - Variable in class etomica.meam.EFSTungsten
display - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
display - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
display - Variable in class etomica.meam.MEAMMd3D
display - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
display - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
display - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
display - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
display - Variable in class etomica.simulation.prototypes.LjMd2D
display - Variable in class etomica.simulation.prototypes.SwMd2D
display - Variable in class etomica.simulation.prototypes.SWMD3D
display - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
display - Static variable in class org.jmol.script.Token
displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
displayBoundary - Variable in class etomica.graphics.DisplayBox
DisplayBox - Class in etomica.graphics: Displays a picture of a box, with configurations of molecules, boundaries, and other objects as appropriate, assuming 2-dimensional system.
DisplayBox(ISimulation, IBox, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBox: Warning: after instantiation, clients using G3DSys may need to toggle display.canvas.setVisible false and then true to fix the 'sometimes gray' bug.
displayBox - Variable in class etomica.graphics.DisplayCanvas
displayBox - Variable in class etomica.modules.crystalviewer.CrystalViewer
displayBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
DisplayBoxCanvas1D - Class in etomica.graphics
DisplayBoxCanvas1D(ISpace, DisplayBox, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvas1D
DisplayBoxCanvas1DBins - Class in etomica.modules.entropylottery: Class used to define canvas onto which configuration is drawn
DisplayBoxCanvas1DBins(DisplayBox, Controller) - Constructor for class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
DisplayBoxCanvas2D - Class in etomica.graphics
DisplayBoxCanvas2D(DisplayBox, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvas2D
DisplayBoxCanvas2DNpTScaling - Class in etomica.normalmode.nptdemo
DisplayBoxCanvas2DNpTScaling(DisplayBox, ISpace, Controller, CoordinateDefinition) - Constructor for class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
DisplayBoxCanvasG3DSys - Class in etomica.graphics
DisplayBoxCanvasG3DSys(ISimulation, DisplayBox, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys
DisplayBoxCanvasG3DSys.OrientedAgentSource - Class in etomica.graphics
DisplayBoxCanvasG3DSys.OrientedFullSite - Class in etomica.graphics
DisplayBoxCanvasG3DSys.OrientedSite - Class in etomica.graphics
displayBoxScaled - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
DisplayBoxSpin2D - Class in etomica.graphics
DisplayBoxSpin2D(DisplayBox, NeighborSiteManager, ISpace, Controller) - Constructor for class etomica.graphics.DisplayBoxSpin2D
DisplayCanvas - Class in etomica.graphics: Superclass for classes that display information from simulation by painting to a canvas.
DisplayCanvas(Controller) - Constructor for class etomica.graphics.DisplayCanvas: Construct a DisplayCanvas using the given controller (which may be null).
displaycellparameters - Static variable in class org.jmol.script.Token
displayCycles - Variable in class etomica.modules.osmosis.Osmosis
displayCycles - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
displayDensity - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
displayDensity - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
displayed - Variable in class etomica.modules.droplet.EllipseDisplayAction
displayEllipse(double) - Method in class etomica.modules.droplet.EllipseDisplayAction
displayList() - Method in class etomica.graphics.SimulationGraphic
displayList() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
displayMaxX - Variable in class org.jmol.util.GData
displayMaxY - Variable in class org.jmol.util.GData
displayMinX - Variable in class org.jmol.util.GData
displayMinY - Variable in class org.jmol.util.GData
displayMoleculeList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
displayMoleculeList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
displayPanel - Variable in class etomica.modules.clustergenerator.MyApplet
DisplayPlot - Class in etomica.graphics: Class for creating a plot of simulation data.
DisplayPlot() - Constructor for class etomica.graphics.DisplayPlot: Creates a plot with a new, empty, DataSinkTable.
DisplayPlot(DataSet) - Constructor for class etomica.graphics.DisplayPlot: Creates a plot using data from the given table.
displayPlot - Variable in class etomica.graphics.EtomicaPlot
DisplayPlot.DataCasterJudgeFunction - Class in etomica.graphics
DisplayPlot.DataWriter - Class in etomica.graphics: Writes a file with the raw data from a plot.
DisplayPlot.PopupListener - Class in etomica.graphics
DisplayPlot.RawDataWindowOpener - Class in etomica.graphics: Opens a window with the raw data from a plot.
DisplayPolytope - Class in etomica.graphics: Displays a picture of a polytope.
DisplayPolytope(Polytope) - Constructor for class etomica.graphics.DisplayPolytope
DisplayPolytope.Applet - Class in etomica.graphics
DisplayPolytopeCanvas2D - Class in etomica.graphics
DisplayPolytopeCanvas2D(DisplayPolytope) - Constructor for class etomica.graphics.DisplayPolytopeCanvas2D
DisplayPolytopeCanvasG3DSys - Class in etomica.graphics
DisplayPolytopeCanvasG3DSys(DisplayPolytope) - Constructor for class etomica.graphics.DisplayPolytopeCanvasG3DSys
DisplayScrollingGraph - Class in etomica.graphics
DisplayScrollingGraph() - Constructor for class etomica.graphics.DisplayScrollingGraph
displaySelectedSpecies(int, int) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
DisplayTable - Class in etomica.graphics: Presents data in a tabular form.
DisplayTable() - Constructor for class etomica.graphics.DisplayTable
DisplayTable(DataSinkTable) - Constructor for class etomica.graphics.DisplayTable
displayTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
displayTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
displayTableEigen - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
displayTableWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
DisplayTextBox - Class in etomica.graphics: A simple display of a single value in a textbox with an associated label.
DisplayTextBox() - Constructor for class etomica.graphics.DisplayTextBox
DisplayTextBox.LabelType - Class in etomica.graphics: Typed constant used to indicate the type of label to be used with the display.
DisplayTextBoxesCAE - Class in etomica.graphics: Display that presents three boxes with the current value, average, and error, respectively, given by an AccumulatorAverage.
DisplayTextBoxesCAE() - Constructor for class etomica.graphics.DisplayTextBoxesCAE
DisplayTimer - Class in etomica.graphics: DisplayBox to present the elapsed time in a molecular dynamics simulation.
DisplayTimer(IntegratorMD) - Constructor for class etomica.graphics.DisplayTimer
dispose() - Method in class etomica.atom.AtomLeafAgentManager: Notifies the AtomAgentManager it should disconnect itself as a listener and release all of its agents.
dispose() - Method in class etomica.atom.AtomTypeAgentManager: Unregisters this class as a listener for AtomType-related events and releases its agents.
dispose() - Method in class etomica.atom.MoleculeAgentManager: Notifies the AtomAgentManager it should disconnect itself as a listener.
dispose() - Method in class etomica.atom.SpeciesAgentManager: Unregisters this class as a listener for AtomType-related events and releases its agents.
dispose() - Method in class etomica.box.BoxAgentManager: Notifies the BoxAgentManager that it should release all agents and stop listening for events from the simulation.
dispose() - Method in class etomica.graphics.DisplayCanvas
dispose() - Method in class etomica.graphics.DisplayTimer: Unhooks the DisplayTimer from the integrator
dispose() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
dispose() - Method in class etomica.nbr.list.NeighborListManager
dispose() - Method in class etomica.util.RandomNumberGeneratorUnix: Cleanup, close the file.
disposeGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
disposeGraphics(Object) - Method in class org.jmol.awt.Platform
disproportionate(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: this function will makes a and b unreactive by setting both to be bonded to themselves (a-a, b-b).
distance - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
distance - Variable in class etomica.virial.ConfigurationClusterMove
distance - Static variable in class org.jmol.script.Token
distance(Point3f) - Method in class org.jmol.util.Point3f: Returns the distance between this point and point p1.
distance(Point4f) - Method in class org.jmol.util.Point4f: Returns the distance between this point and point p1.
distanceSquared(Point3f) - Method in class org.jmol.util.Point3f: Computes the square of the distance between this point and point p1.
distanceTo(IVector) - Method in class etomica.math.geometry.Plane: Perpendicular distance from the plane to the given point.
distanceTo(IVector) - Method in class etomica.math.geometry.Polyhedron: Returns the perpendicular distance to the nearest face of the polyhedron.
distanceTo(IVector) - Method in class etomica.modules.pistoncylinder.PistonPlane
distanceTo(IVector) - Method in class etomica.modules.sam.WallPlane
distanceToPlane(Point4f, Point3f) - Static method in class org.jmol.util.Measure
distanceToPlane(Vector3f, float, Point3f) - Static method in class org.jmol.util.Measure
distanceToPlaneD(Point4f, float, Point3f) - Static method in class org.jmol.util.Measure
distPol - Variable in class etomica.models.water.P2WaterSzalewicz
Distribution(ISpace, double, double) - Constructor for class etomica.statmech.MaxwellBoltzmann.Distribution
div(Complex) - Method in class etomica.math.Complex: Division of Complex numbers (doesn't change this Complex number).
div(Quaternion) - Method in class org.jmol.util.Quaternion
div(Quaternion[], Quaternion[], int, boolean) - Static method in class org.jmol.util.Quaternion
divide(Coefficient) - Method in interface etomica.graph.model.Coefficient
divide(Coefficient) - Method in class etomica.graph.model.impl.CoefficientImpl
divide(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd: Divide by another square root.
divide(BigInteger) - Method in class etomica.veos.bigdecimal.BigSurd: Divide by an integer.
divide(int) - Method in class etomica.veos.bigdecimal.BigSurd: Divide by an integer.
divide(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Integer division through another positive integer.
divide(Rational) - Method in class etomica.veos.bigdecimal.Rational: Divide by another fraction.
divide(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Divide by an integer.
divide(int) - Method in class etomica.veos.bigdecimal.Rational: Divide by an integer.
divideAndRemainder(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Divide by another polynomial.
divideRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divideRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divideRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divideRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divideRound(BigInteger, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divideRound(BigInteger, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divideRound(int, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Divide and round.
divisor - Variable in class etomica.potential.Potential0Lrc
divisors(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Compute the list of positive divisors.
divisors() - Method in class etomica.veos.bigdecimal.Ifactor: The set of positive divisors.
divLeft(Quaternion) - Method in class org.jmol.util.Quaternion
DLGA(double) - Static method in class etomica.math.Gamma
DLJ_NVT_1site - Class in etomica.AlkaneEH: Canonical ensemble Monte Carlo simulation (NVT) calculate dielectric constant epsilon for dipolar LJ model
DLJ_NVT_1site(Space, int, double, double, double, double, double, double, double) - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site
DLJ_NVT_1site - Class in etomica.dielectric: Canonical ensemble Monte Carlo simulation (NVT) calculate dielectric constant epsilon for dipolar LJ model
DLJ_NVT_1site(Space, int, double, double, double, double, double, double, double) - Constructor for class etomica.dielectric.DLJ_NVT_1site
DLJ_NVT_1site.DipoleSourceDLJ - Class in etomica.AlkaneEH
DLJ_NVT_1site.DipoleSourceDLJ - Class in etomica.dielectric
DLJ_NVT_1site.Param - Class in etomica.AlkaneEH
DLJ_NVT_1site.Param - Class in etomica.dielectric
dmptab - Variable in class etomica.models.water.P2WaterSzalewicz
dn - Variable in class etomica.potential.P3HydrogenManzhos
dna - Static variable in class org.jmol.script.Token
doAction(IAction) - Method in class etomica.graphics.Device: Method called by subclasses to execute the action of the device.
doAction(IAction) - Method in class etomica.graphics.DeviceSlider
doActionNow(IAction) - Method in class etomica.action.activity.Controller: Pauses current activity, executes given action, then resumes current activity.
doActionNow(IAction) - Method in interface etomica.action.activity.IController: Pauses current activity, executes given action, then resumes current activity.
doAdjustStepFrac - Variable in class etomica.overlap.IntegratorOverlap
doAdjustStepsOnTime - Variable in class etomica.overlap.IntegratorOverlap
doAggressiveAdjustStepFrac - Variable in class etomica.overlap.IntegratorOverlap
doApplyPBC - Variable in class etomica.action.WriteConfiguration
doApplyPBC - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
doApplyPBC - Variable in class etomica.nbr.cell.NeighborCellManager
doApplyPBC - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
doApplyPBC - Variable in class etomica.nbr.list.NeighborListManager
doAveraging - Variable in class etomica.util.HistogramNotSoSimple
doAvgDef - Variable in class etomica.normalmode.DataSourceFE
doBlockSum() - Method in class etomica.data.AccumulatorAverageCollapsing: Performs the block sum after blockSize calls to addData.
doBlockSum() - Method in class etomica.data.AccumulatorAverageCovariance
doBlockSum() - Method in class etomica.data.AccumulatorAverageFixed: Performs the block sum after blockSize calls to addData.
doBlockSum() - Method in class etomica.data.AccumulatorAverageFixedOutputFile: Performs the block sum after blockSize calls to addData.
doBlockSum() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
doCaching - Variable in class etomica.virial.ClusterSum
doCaching - Variable in class etomica.virial.ClusterSumPolarizable
doCaching - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
doCaching - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
doCaching - Variable in class etomica.virial.ClusterWheatleySoft
doCaching - Variable in class etomica.virial.ClusterWheatleySoftBD
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.data.meter.PotentialCalculationRDF
doCalculation(IAtomList, IPotential) - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
doCalculation(IAtomList, IPotential) - Method in class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff: Adds to the energy sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff: Adds to the energy sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoffLS: Adds to the energy sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedvirial.MappedUpotential
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce: Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce: Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationEFSSP
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationLJSP
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuper: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCutLS: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in interface etomica.potential.PotentialCalculation: Method giving the specific calculation performed by this class.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationEnergySum: Adds to the energy sum the energy values obtained from application of the given potential to the atoms.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationEnergySum: Adds to the energy sum the energy values obtained from application of the given potential to the molecules.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal: Adds to the energy sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal: Adds to the energy sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationForcePressureSum: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationForceSum: Adds forces due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationHyperVirialSum: Adds to the virial sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in interface etomica.potential.PotentialCalculationMolecular: Method giving the specific calculation performed by this class.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationPhiSum
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationPhiSum
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationPressureTensor: Adds the pressure tensor contribution based on the forces acting on each pair of atoms produced by the iterator.
doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationTorqueSum: Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationTorqueSum: Adds forces and torques due to given potential acting on the atoms produced by the iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationVirialSum: Adds to the virial sum the energy values obtained from application of the given potential to the atoms produced by the given iterator.
doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
doClear - Variable in class etomica.graphics.DisplayPlot
doConfigButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
doContinue() - Method in class etomica.action.Activity
doCopy - Variable in class etomica.graph.iterators.IteratorWrapper
doCorrection - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
doCorti - Variable in class etomica.normalmode.MCMoveVolumeSolid
doCov - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
doCov - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
doCov - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
doD2 - Variable in class etomica.normalmode.MeterSolidDA
doD2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
dodebug - Static variable in class etomica.association.MCMoveAtomSmer
dodebug - Static variable in class etomica.association.MCMoveMoleculeSmer
dodebug - Static variable in class etomica.association.MCMoveVolumeAssociated
dodebug - Static variable in class etomica.association.MCMoveVolumeAssociatedMolecule
dodebug - Static variable in class etomica.integrator.IntegratorMC
doDensityInput - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
doDiff - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagrams
doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagramsMix2
doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagramsPT
doDouble - Variable in class etomica.modules.rheology.MeterNormalStress
doDown - Variable in class etomica.lattice.RectangularLatticeNbrIterator
doEigenDecompose(double[][], String) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
doEigenDecompose(double[][], String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
doEigenDecomposeAndFile(double[][], String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
doEnforceBounds - Variable in class etomica.data.DataSourceUniform
doExchange - Variable in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
doExchange - Variable in class etomica.virial.cluster.VirialDiagrams
doExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
doExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT
doExchangeCondensing - Variable in class etomica.virial.cluster.VirialDiagrams
doExchangeCondensing - Variable in class etomica.virial.cluster.VirialDiagramsPT
doExchangeF - Variable in class etomica.virial.cluster.VirialDiagrams
doExchangeF - Variable in class etomica.virial.cluster.VirialDiagramsPT
doExcludeNonNeighbors - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
doExcludeNonNeighbors - Variable in class etomica.normalmode.MCMoveAtomCoupled
doExcludeNonNeighbors - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
doExp - Variable in class etomica.virial.cluster.VirialDiagramsPT
doExp - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
doExpDensityprofile - Variable in class etomica.virial.cluster.ExternalVirialDiagrams
doFancyMonoclinic - Static variable in class etomica.normalmode.HSDimerNPT
doFancyOriented - Static variable in class etomica.normalmode.HSDimerNPT
doFastButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
doFindMinimum(double[], double[], double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
doFindMinimum(double[], double[], double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
doFindMinimum(double[], double[], double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
doFindMinimum(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
doFit(double[], double[]) - Method in class etomica.modules.interfacial.FitTanh
doFit(double[], double[]) - Method in class etomica.surfacetension.FitTanh
doFit(double[], double[]) - Static method in class etomica.util.numerical.LinearFit
doFit(double[], double[], double[]) - Static method in class etomica.util.numerical.LinearFit
doFit(int, double[], double[]) - Static method in class etomica.util.numerical.PolynomialFit: Perform polynomial fit of the given order.
doFit(int, double[], double[], double[]) - Static method in class etomica.util.numerical.PolynomialFit: Perform polynomial fit of the given order with the given weights (w).
doFlip(IMolecule) - Method in class etomica.association.BiasVolume2SiteAceticAcid
doFlip(IMolecule) - Method in class etomica.association.BiasVolumeAceticAcid
doGlobalMoves() - Method in class etomica.integrator.IntegratorManagerMC: Method to select and perform an elementary Monte Carlo move.
doGoDown - Variable in class etomica.atom.iterator.MpiIntraspecies1A
doGoDown - Variable in class etomica.atom.iterator.TripletInnerSequential
doGoUp - Variable in class etomica.atom.iterator.TripletInnerSequential
doGradientNoShift(IVector, IVector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
doGradientShift(IVector, IVector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
doGraphics - Static variable in class etomica.normalmode.HSDimerNPT
doHB - Variable in class etomica.virial.cluster.VirialDiagrams
doHB - Variable in class etomica.virial.cluster.VirialDiagramsPT
doHist - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
doHist - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
doHist - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
doHist - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
doHist - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
doHist - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
doHist - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
doHist - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
doHist - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
doHist - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
doHist - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
doHist - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
doHist - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
doHist - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
doHistory - Variable in class etomica.meam.EFSTungsten.Params
doIgnoreRefAvg - Variable in class etomica.virial.overlap.DataVirialOverlap
doIncludeACInError - Variable in class etomica.data.AccumulatorAverage
doIncludePair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
doIncludePair - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
doInterpolateHole() - Method in class etomica.util.numerical.AkimaSplineSmoother
doInterpolateHole2() - Method in class etomica.util.numerical.AkimaSplineSmoother
doInterpolation(double[]) - Method in class etomica.util.numerical.AkimaSpline
doInterpolationDy(double[]) - Method in class etomica.util.numerical.AkimaSpline
doit(NormalModes, int, double, int) - Static method in class etomica.normalmode.CalcHarmonicA
doit(String, int) - Static method in class etomica.normalmode.NormalModeEigenGetter
doit(String) - Static method in class etomica.paracetamol.NormalModeEigenGetter
doJustTilt - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagrams
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsMix
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsMix2
doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsPT
doLatticeSum - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
doLatticeSum - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
doLatticeSum - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
doLogLevel(boolean) - Static method in class org.jmol.util.Logger: Indicates if the level is logged.
doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagrams
doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagramsMix
doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagramsPT
doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagrams
doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagramsMix
doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagramsPT
doMulti - Variable in class etomica.virial.ClusterWheatleyMultibody
doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
doMultiFromPair - Variable in class etomica.virial.cluster.VirialDiagrams
doMultiFromPair - Variable in class etomica.virial.cluster.VirialDiagramsPT
doNBodyStuff(IMolecule, PotentialCalculation, int, IPotentialMolecular, NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Invokes the PotentialCalculationMolecular for the given Molecule with its up and down neighbors as a single MoleculeSet.
doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList: Invokes the PotentialCalculation for the given Atom with its up and down neighbors as a single AtomSet.
doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic) - Method in class etomica.threaded.atom.PotentialMasterListWorker
doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic) - Method in class etomica.threaded.domain.PotentialMasterListWorker
done - Variable in class etomica.atom.iterator.ANIntragroupExchange
doNegativeExchange - Variable in class etomica.virial.cluster.VirialDiagrams
doNegativeExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT
doNMoleculeSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
doNonEquilibrium - Variable in class etomica.potential.PotentialCalculationPressureTensor
DooDad(int) - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.DooDad
doOverwrite - Variable in class etomica.normalmode.WriteS
doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvas1D: doPaint is the method that handles the drawing of the box to the screen.
doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvas2D: Method that handles the drawing of the box to the screen.
doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
doPaint(Graphics) - Method in class etomica.graphics.DisplayCanvas
doPaint(Graphics) - Method in class etomica.graphics.DisplayPolytopeCanvas2D: doPaint is the method that handles the drawing of the box to the screen.
doPaint(Graphics) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
doPaint(Graphics) - Method in class etomica.graphics.DisplayScrollingGraph
doPaint(Graphics) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins: doPaint is the method that handles the drawing of the box to the screen.
doParse(String, ISpace) - Static method in class etomica.virial.simulations.ShapeParser
doParseArgs(ParameterBase, String[]) - Static method in class etomica.util.ParseArgs
doPBC - Variable in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
doPBC - Variable in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
doRandStep() - Method in class etomica.util.numerical.AkimaSplineSmoother
doRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
doRealSum - Variable in class etomica.potential.EwaldSummation
doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagrams
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsMix
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsMix2
doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsPT
doReeHoover - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
doReeHoover - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
doReeHoover - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
doResetFilter - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
doResize - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
doReweight - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
doReweight - Variable in class etomica.normalmode.SimLJVacancy.LJParams
doReweight - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
doReweight - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
doRing - Variable in class etomica.virial.ClusterChainSoft
doRot - Static variable in class etomica.normalmode.HSDimerNPT
doRotation(int, IMolecule, double, double) - Method in class etomica.models.water.P2Water4PSoft
doRotationTransform(double, double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
doScaling - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
doScaling - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
doScaling - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
doSearch(int, int) - Method in class etomica.virial.ClusterSumMultibody
doSecDerXrNoShift(IVector, IVector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
doSecDerXrRotRotNoShift(IVector, IVector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
doSecDerXrRotRotWShift(IVector, IVector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
doSecDerXrWShift(IVector, IVector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
doSerialize - Variable in class etomica.util.EventManager.Linker
doShape - Static variable in class etomica.normalmode.HSDimerNPT
doShiftInitY() - Method in class etomica.util.numerical.AkimaSplineSmootherDy
doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
doShortcut - Variable in class etomica.virial.cluster.VirialDiagrams
doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsMix
doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsMix2
doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsPT
doShortcut - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
doShortcut - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
doShowCurrent - Variable in class etomica.graphics.DisplayTextBoxesCAE
doStatistics - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
doStep() - Method in interface etomica.api.IIntegrator: Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
doStep() - Method in class etomica.integrator.Integrator
doStep() - Method in class etomica.util.numerical.AkimaSplineSmoother
doStep() - Method in class etomica.util.numerical.AkimaSplineSmootherDy
doStepInternal() - Method in class etomica.action.IntegratorDimerApproach
doStepInternal() - Method in class etomica.dimer.IntegratorDimerMin
doStepInternal() - Method in class etomica.dimer.IntegratorDimerRT
doStepInternal() - Method in class etomica.dimer.IntegratorEnergyMap
doStepInternal() - Method in class etomica.integrator.Integrator: Performs the elementary integration step, such as a molecular dynamics time step, or a Monte Carlo trial.
doStepInternal() - Method in class etomica.integrator.IntegratorAnalytic
doStepInternal() - Method in class etomica.integrator.IntegratorConNVT
doStepInternal() - Method in class etomica.integrator.IntegratorGear4
doStepInternal() - Method in class etomica.integrator.IntegratorGear4NPH
doStepInternal() - Method in class etomica.integrator.IntegratorHard: Steps all atoms across time interval timeStep, handling all intervening collisions.
doStepInternal() - Method in class etomica.integrator.IntegratorManagerMC: Performs a Monte Carlo trial that attempts to swap the configurations between two "adjacent" boxes, or instructs all integrators to perform a single doStep.
doStepInternal() - Method in class etomica.integrator.IntegratorMC: Method to select and perform an elementary Monte Carlo move.
doStepInternal() - Method in class etomica.integrator.IntegratorMD
doStepInternal() - Method in class etomica.integrator.IntegratorRigidIterative
doStepInternal() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerlet
doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerletRattle
doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerletShake
doStepInternal() - Method in class etomica.integrator.IntegratorVerlet
doStepInternal() - Method in class etomica.kmc.IntegratorKMC
doStepInternal() - Method in class etomica.kmc.IntegratorKMCCluster
doStepInternal() - Method in class etomica.modules.adsorption.IntegratorHybrid
doStepInternal() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
doStepInternal() - Method in class etomica.modules.droplet.IntegratorDroplet
doStepInternal() - Method in class etomica.modules.joulethomson.IntegratorJT
doStepInternal() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
doStepInternal() - Method in class etomica.modules.rheology.IntegratorPolymer
doStepInternal() - Method in class etomica.modules.sam.IntegratorVelocityVerletSAM
doStepInternal() - Method in class etomica.normalmode.IntegratorHarmonic
doStepInternal() - Method in class etomica.overlap.IntegratorOverlap
doStepInternal() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
doStepInternal() - Method in class etomica.thermointegration.IntegratorThermodynamic: Performs a step in the subIntegrator.
doStepInternal() - Method in class etomica.tmmc.IntegratorTMMC: Method to select and perform an elementary Monte Carlo move.
doStepInternal() - Method in class etomica.util.numerical.AkimaSplineSmootherApp.IntegratorSmoother
doStepInternal() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.IntegratorSmoother
doStepInternal() - Method in class etomica.virial.overlap.IntegratorOverlap
doStrictBlockData - Variable in class etomica.data.AccumulatorAverageFixed
doSubtractComb - Variable in class etomica.normalmode.DataSourceFE
doSum112(double[], double[], double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum113(double[], double[], double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum122(double[], double[], double[], double[], double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum644(double[], double[], double[], double[], double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum660(double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum734(double[], double[], double[], double[], double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum770(double[], double[], double[]) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum833(double[], double[], double[], double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSum860(double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
doSums(double[], double) - Method in class etomica.data.AccumulatorAverageCollapsingLog: Performs the block sum after
doSurfacetension - Variable in class etomica.virial.cluster.ExternalVirialDiagrams
doSwap - Variable in class etomica.atom.iterator.ApiInnerVariable
doSwap - Variable in class etomica.atom.iterator.MpiInnerVariable
dot(IVector) - Method in interface etomica.api.IVector: Returns the dot product of this vector with the given one.
dot(IVector) - Method in class etomica.space1d.Vector1D
dot(IVector) - Method in class etomica.space2d.Vector2D
dot(IVector) - Method in class etomica.space3d.Vector3D
dot(IVector) - Method in class etomica.spaceNd.VectorND
dot(Quaternion) - Method in class org.jmol.util.Quaternion
dot(Vector3f) - Method in class org.jmol.util.Vector3f: Computes the dot product of the this vector and vector v.
dotdensity - Static variable in class org.jmol.script.Token
doThermostat() - Method in class etomica.integrator.IntegratorMD: thermostat implementation.
doThermostat() - Method in class etomica.normalmode.IntegratorHardMDMC
doThermostat() - Method in class etomica.normalmode.IntegratorHarmonic
doThermostatInternal() - Method in class etomica.integrator.IntegratorMD: Fires the thermostat if the appropriate interval has been reached.
doThermostatInternal() - Method in class etomica.modules.rheology.IntegratorPolymer
doTotal - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
doTotal - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
doTotal - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
doTotal - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
doTotal - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
doTransform(IMolecule, IVector, IVector, double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
doTransform(IMolecule, IVector, IVector, double) - Method in class etomica.association.BiasVolumeAceticAcid
doTransform(IMolecule, IVector) - Method in class etomica.association.MCMoveBiasUBMolecule
doTransform(IAtom) - Method in class etomica.association.MCMoveDimerRotate
doTransform(IAtomOriented) - Method in class etomica.association.MCMoveSmerRotate
doTransform(IAtom) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
doTransform() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
doTransform(IMolecule, IBoundary, Tensor) - Static method in class etomica.models.clathrates.MinimizationTIP4P
doTransform() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
doTransform() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
doTransform(IMolecule, IVector) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
doTransform(IMolecule, IAtomPositionDefinition, Tensor) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
doTransform(IMolecule, IAtomPositionDefinition, Tensor) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
doTransform(IMolecule, IVector, RotationTensor) - Static method in class etomica.models.water.OrientationCalcWater3P
doTransform(IMolecule, IVector, RotationTensor) - Static method in class etomica.models.water.OrientationCalcWater4P
doTransform(IMolecule) - Method in class etomica.models.water.P2Water4PSoft
doTransform() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
doTransform(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
doTransform(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
doTransformMolec(int, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
doTransformPhi(IMolecule) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
doTransformTheta(IMolecule, double, double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
doTransformToInitial(int, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
doTrial() - Method in class etomica.association.MCMoveAtomSmer
doTrial() - Method in class etomica.association.MCMoveBiasUB
doTrial() - Method in class etomica.association.MCMoveBiasUBMolecule
doTrial() - Method in class etomica.association.MCMoveDimer: Method to perform trial move.
doTrial() - Method in class etomica.association.MCMoveDimerRotate: Method to perform trial move.
doTrial() - Method in class etomica.association.MCMoveMoleculeRotateAssociated
doTrial() - Method in class etomica.association.MCMoveMoleculeSmer
doTrial() - Method in class etomica.association.MCMoveRotateAssociated
doTrial() - Method in class etomica.association.MCMoveSmer: Method to perform trial move.
doTrial() - Method in class etomica.association.MCMoveSmerRotate: Method to perform trial move.
doTrial() - Method in class etomica.association.MCMoveVolumeAssociated
doTrial() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
doTrial() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled: Method to perform trial move.
doTrial() - Method in class etomica.freeenergy.npath.MCMoveAtomNPath: Method to perform trial move.
doTrial() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap: Method to perform trial move.
doTrial() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
doTrial() - Method in class etomica.integrator.mcmove.MCMove: Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveAtom: Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveAtomInRegion
doTrial() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
doTrial() - Method in class etomica.integrator.mcmove.MCMoveDimer: Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate: Method to perform trial move.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Chooses and performs with equal probability an elementary molecule insertion or deletion.
doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
doTrial() - Method in class etomica.integrator.mcmove.MCMoveMolecule
doTrial() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
doTrial() - Method in class etomica.integrator.mcmove.MCMoveRotate
doTrial() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
doTrial() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
doTrial() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
doTrial() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
doTrial() - Method in class etomica.integrator.mcmove.MCMoveVolume
doTrial() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
doTrial() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
doTrial() - Method in class etomica.interfacial.MCMoveAtomNbr
doTrial() - Method in class etomica.models.hexane.MCMoveCBMC
doTrial(IMolecule) - Method in class etomica.models.hexane.MCMoveCBMC
doTrial() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
doTrial() - Method in class etomica.models.hexane.MCMoveReptate: method to perform a trial move.
doTrial() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
doTrial() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
doTrial() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
doTrial() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
doTrial() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
doTrial() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
doTrial() - Method in class etomica.modules.adsorption.MyMCMove: Chooses and performs with equal probability an elementary molecule insertion or deletion.
doTrial() - Method in class etomica.modules.dcvgcmd.MyMCMove: Chooses and performs with equal probability an elementary molecule insertion or deletion.
doTrial() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent: Method to perform trial move.
doTrial() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
doTrial() - Method in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
doTrial() - Method in class etomica.modules.vle.MCMoveVolumeExchangeVLE
doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupled: Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet: Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella: Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveAtomSuperBox: Method to perform trial move.
doTrial() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
doTrial() - Method in class etomica.normalmode.MCMoveHarmonic
doTrial() - Method in class etomica.normalmode.MCMoveHarmonicEin
doTrial() - Method in class etomica.normalmode.MCMoveHarmonicStep
doTrial() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
doTrial() - Method in class etomica.normalmode.MCMovePhaseAngle
doTrial() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
doTrial() - Method in class etomica.normalmode.MCMoveSingleMode
doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
doTrial() - Method in class etomica.normalmode.MCMoveVolumeSolid
doTrial() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
doTrial() - Method in class etomica.normalmode.MCMoveWV
doTrial() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
doTrial() - Method in class etomica.spin.MCMoveSpinFlip
doTrial() - Method in class etomica.virial.MCMoveChangeBondLength
doTrial() - Method in class etomica.virial.MCMoveClusterAngleBend
doTrial() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
doTrial() - Method in class etomica.virial.MCMoveClusterAtom
doTrial() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
doTrial() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSChain
doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSRing
doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSTree
doTrial() - Method in class etomica.virial.MCMoveClusterAtomMulti
doTrial() - Method in class etomica.virial.MCMoveClusterAtomQ
doTrial() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
doTrial() - Method in class etomica.virial.MCMoveClusterDiagram
doTrial() - Method in class etomica.virial.MCMoveClusterMolecule
doTrial() - Method in class etomica.virial.MCMoveClusterMoleculeLayerMove
doTrial() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
doTrial() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
doTrial() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
doTrial() - Method in class etomica.virial.MCMoveClusterReptateMulti
doTrial() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrow
doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
doTrial() - Method in class etomica.virial.MCMoveClusterRingScale
doTrial() - Method in class etomica.virial.MCMoveClusterRotateCH3
doTrial() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
doTrial() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
doTrial() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
doTrial() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
doTrial() - Method in class etomica.virial.MCMoveClusterTorsionMulti
doTrial() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
doTrial() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
doTrial() - Method in class etomica.virial.MCMoveClusterWiggleMulti
doTrial() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
dots - Static variable in class org.jmol.script.Token
dotscale - Static variable in class org.jmol.script.Token
dotsselectedonly - Static variable in class org.jmol.script.Token
dotsurface - Static variable in class org.jmol.script.Token
DoubleAssociationSitesFluid2Pt - Class in etomica.virial.simulations
DoubleAssociationSitesFluid2Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt
DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
DoubleAssociationSitesFluid3Pt - Class in etomica.virial.simulations
DoubleAssociationSitesFluid3Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt
DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
DoubleAssociationSitesFluid4Pt - Class in etomica.virial.simulations: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's double attraction-site model, hyper-point diagram 4 point diagram calculation
DoubleAssociationSitesFluid4Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt
DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
DoubleIntegral - Class in etomica.models.oneDHardRods
DoubleIntegral(double, double, double, double, int, int) - Constructor for class etomica.models.oneDHardRods.DoubleIntegral
DoubleIntegralEtas - Class in etomica.models.oneDHardRods: Please note this class is specifically designed to integrate for 2 or 3 rod systems, with one rod per cell.
DoubleIntegralEtas(int, double, double) - Constructor for class etomica.models.oneDHardRods.DoubleIntegralEtas
doubleLength(Object) - Static method in class org.jmol.util.ArrayUtil: Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
doubleLengthBool(boolean[]) - Static method in class org.jmol.util.ArrayUtil
doubleLengthByte(byte[]) - Static method in class org.jmol.util.ArrayUtil
doubleLengthF(float[]) - Static method in class org.jmol.util.ArrayUtil
doubleLengthI(int[]) - Static method in class org.jmol.util.ArrayUtil
doubleLengthS(String[]) - Static method in class org.jmol.util.ArrayUtil
doubleLengthShort(short[]) - Static method in class org.jmol.util.ArrayUtil
DoubleRange - Class in etomica.util
DoubleRange(double, double) - Constructor for class etomica.util.DoubleRange: Constructs the range defined by given values.
doubleValue() - Method in class etomica.veos.bigdecimal.BigSurd: Return a double value representation.
doubleValue() - Method in class etomica.veos.bigdecimal.BigSurdVec: Construct an approximate floating point representation
doubleValue() - Method in class etomica.veos.bigdecimal.Rational: Return a double value representation.
DoubleWrapper() - Constructor for class etomica.nbr.CriterionPositionWall.DoubleWrapper
doUp - Variable in class etomica.lattice.RectangularLatticeNbrIterator
doUpdate() - Method in class etomica.graphics.DeviceBox: Updates the display of the box with the current value given by the modifier.
doUpdate() - Method in class etomica.graphics.DeviceSlider
doUpdate() - Method in class etomica.graphics.DeviceSpinner
doUpdate() - Method in class etomica.graphics.DisplayPlot: Redraws the plot.
doUpdate() - Method in class etomica.graphics.DisplayPolytope
doUpdate() - Method in class etomica.graphics.DisplayScrollingGraph
doUpdate() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
doUpdateFMulti(int, IMoleculeList, CoordinatePairSet) - Method in class etomica.virial.ClusterSumMultibody
doWait() - Method in class etomica.action.Activity: Method to put activity in a condition of being paused.
doWheatley - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
doWheatley - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
doWheatley - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
doWiggle - Variable in class etomica.virial.GUI.models.ModelSimulationEnvironment
doWiggle - Variable in class etomica.virial.simulations.SimulationVirial
doWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
DOWN - Static variable in class etomica.atom.iterator.IteratorDirective.Direction
downList - Variable in class etomica.integrator.IntegratorHard
downList - Variable in class etomica.nbr.list.AtomNeighborLists
downList - Variable in class etomica.nbr.list.molecule.MoleculeNeighborLists
dP - Variable in class etomica.normalmode.MeterSolidProps
dP - Variable in class etomica.normalmode.MeterSolidPropsLJ
dP - Variable in class etomica.normalmode.PotentialCalculationLJSP
dPdRho(double) - Method in class etomica.modules.adsorption.EOSSWPatel
dPdRho(double) - Method in class etomica.modules.adsorption.VEOS3SW
dphi_du(int[], double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
dphi_du(int[], double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
dPlot - Variable in class etomica.modules.vle.B2Fit
dPlot - Variable in class etomica.modules.vle.B2Fit.FunctionB2LJQ
dPlot - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
dpolx - Static variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
dpVirialOverlap - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
dqdVCalc(double, int) - Method in class etomica.veos.Ushcats
dr - Variable in class etomica.association.AssociationHelperBranched
dr - Variable in class etomica.association.AssociationHelperDouble
dr - Variable in class etomica.association.AssociationHelperMolecule
dr - Variable in class etomica.association.MCMoveAtomMonomer
dr - Variable in class etomica.association.MCMoveAtomSmer
dr - Variable in class etomica.association.MCMoveBiasUB
dr - Variable in class etomica.association.MCMoveDimer
dr - Variable in class etomica.association.MCMoveDimerRotate
dr - Variable in class etomica.association.MCMoveMoleculeMonomer
dr - Variable in class etomica.association.MCMoveMoleculeSmer
dr - Variable in class etomica.association.MCMoveRotateAssociated
dr - Variable in class etomica.association.MCMoveSmer
dr - Variable in class etomica.association.MCMoveSmerRotate
dr - Variable in class etomica.association.MCMoveVolumeAssociated
dr - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
dr - Variable in class etomica.atom.AtomPositionGeometricCenterPBC
dr - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
dr - Variable in class etomica.data.meter.PotentialCalculationRDF
dr - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
dr - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
dr - Variable in class etomica.graphics.ColorSchemeOverlap
dr - Variable in class etomica.integrator.IntegratorVelocityVerletShake
dr - Variable in class etomica.integrator.mcmove.MCMoveDimer
dr - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
dr - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
dr - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
dr - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
dr - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
dr - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
dr - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
dr - Variable in class etomica.mappedvirial.MappedUpotential
dr - Variable in class etomica.mappedvirial.MeterMeanForce
dr - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
dr - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
dr - Variable in class etomica.meam.PotentialCuLREP
dr - Variable in class etomica.meam.PotentialEFS
dr - Variable in class etomica.meam.PotentialFeEAM
dr - Variable in class etomica.meam.PotentialFeEAM_LS
dR - Variable in class etomica.meam.PotentialFeEAM_LS
dr - Variable in class etomica.models.water.P2Water4PSoft
dr - Variable in class etomica.modules.colloid.MeterEnd2End
dr - Variable in class etomica.modules.droplet.IntegratorDroplet
dr - Variable in class etomica.modules.droplet.MeterDeformation
dr - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
dr - Variable in class etomica.modules.interfacial.MeterOrientation
dr - Variable in class etomica.modules.mu.P1MagicWall
dr - Variable in class etomica.modules.rheology.IntegratorPolymer
dr - Variable in class etomica.modules.rheology.MeterEndToEnd
dr - Variable in class etomica.modules.rheology.MeterNormalStress
dr - Variable in class etomica.modules.rheology.MeterViscosity
dr - Variable in class etomica.modules.sam.MeterTilt
dr - Variable in class etomica.nbr.CriterionPositionWall
dr - Variable in class etomica.nbr.CriterionSimple
dr - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
dr - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
dr - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
dr - Variable in class etomica.normalmode.MCMoveVolumeSolid
dr - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
dr - Variable in class etomica.normalmode.MeterDADB
dr - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
dr - Variable in class etomica.normalmode.MeterDisplacementRMS
dr - Variable in class etomica.normalmode.MeterMaxExpansion
dr - Variable in class etomica.normalmode.MeterPhiDeviation
dr - Variable in class etomica.normalmode.MeterSolidDA
dr - Variable in class etomica.normalmode.MeterSolidMirror
dr - Variable in class etomica.normalmode.MeterSolidProps
dr - Variable in class etomica.normalmode.MeterSolidPropsLJ
dr - Variable in class etomica.normalmode.MeterThetaDeviation
dr - Variable in class etomica.normalmode.MeterTilt
dr - Variable in class etomica.normalmode.MeterTiltHistogram
dr - Variable in class etomica.normalmode.MeterTiltRotation
dr - Variable in class etomica.normalmode.MeterTiltRotationHistogram
dr - Variable in class etomica.normalmode.MeterTiltRotationStdev
dr - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
dr - Variable in class etomica.normalmode.P2XOrder
dr - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
dr - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
dr - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
dr - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
dr - Variable in class etomica.potential.P2HydrogenHinde
dr - Variable in class etomica.potential.P2HydrogenHindeAtomic
dr - Variable in class etomica.potential.P2HydrogenHindePatkowski
dr - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
dr - Variable in class etomica.potential.P2HydrogenPatkowski
dr - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
dr - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
dr - Variable in class etomica.potential.P2MoleculeTruncated
dr - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
dr - Variable in class etomica.potential.P2ReactionFieldDipole
dr - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
dr - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
dr - Variable in class etomica.potential.P2SoftTruncated
dr - Variable in class etomica.potential.P2SpheroPolyhedron
dr - Variable in class etomica.potential.P3HydrogenATM
dR - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
dr - Variable in class etomica.potential.Potential2HardSpherical
dr - Variable in class etomica.potential.Potential2SoftSpherical
dr - Variable in class etomica.potential.Potential2SoftSphericalLS
dr - Variable in class etomica.potential.PotentialCalculationPhiSum
dr - Variable in class etomica.virial.CoordinatePairLeafSet
dr - Variable in class etomica.virial.CoordinatePairMoleculeSet
dr - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
dr - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
dr - Variable in class etomica.virial.MCMoveClusterAtomHSChain
dr - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
dr - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
dr - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
dr - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
dr0 - Variable in class etomica.models.water.P2Water4PSoft
dr01 - Variable in class etomica.potential.P2Exp6
dr01 - Variable in class etomica.potential.P2Exp6Buckingham
dr01 - Variable in class etomica.potential.P2LennardJonesDreiding
dr1 - Variable in class etomica.integrator.IntegratorGear4.Agent
dr1 - Variable in class etomica.models.nitrogen.P2Nitrogen
dr1 - Variable in class etomica.models.water.P2Water4PSoft
dr1 - Variable in class etomica.potential.P2ReactionFieldDipole
dr1 - Variable in class etomica.potential.P3AxilrodTeller
dr1 - Variable in class etomica.potential.P3Induction
dr12 - Variable in class etomica.potential.P3BondAngle
dr12 - Variable in class etomica.potential.P3BondAngleDreiding
dr12 - Variable in class etomica.potential.P4TorsionDreiding
dr2 - Variable in class etomica.association.MCMoveSmerRotate
dr2 - Variable in class etomica.association.MCMoveVolumeAssociated
dr2 - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
dr2 - Variable in class etomica.integrator.IntegratorGear4.Agent
dr2 - Variable in class etomica.models.nitrogen.P2Nitrogen
dr2 - Variable in class etomica.potential.P3AxilrodTeller
dr2 - Variable in class etomica.potential.P3Induction
dr21 - Variable in class etomica.potential.P4BondTorsion
dr21 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
dr21 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
dr21 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
dr23 - Variable in class etomica.potential.P3BondAngle
dr23 - Variable in class etomica.potential.P3BondAngleDreiding
dr23 - Variable in class etomica.potential.P4BondTorsion
dr23 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
dr23 - Variable in class etomica.potential.P4TorsionDreiding
dr23 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
dr23 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
dr3 - Variable in class etomica.integrator.IntegratorGear4.Agent
dr34 - Variable in class etomica.potential.P4BondTorsion
dr34 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
dr34 - Variable in class etomica.potential.P4TorsionDreiding
dr34 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
dr34 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
dr4 - Variable in class etomica.integrator.IntegratorGear4.Agent
drA - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
drA - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
drA - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
dra - Variable in class etomica.potential.P4TorsionDreiding
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHe
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHe
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
dragselected - Static variable in class org.jmol.script.Token
draw() - Method in class etomica.graph.viewer.GraphMap
draw(Graphics, int[], double) - Method in interface etomica.graphics.Drawable
draw(Graphics, int[], double) - Method in class etomica.modules.osmosis.Osmosis.MyWall
draw(Graphics, int[], double) - Method in class etomica.potential.P1HardBoundary
draw(Graphics, int[], double) - Method in class etomica.potential.P1HardMovingBoundary
draw() - Method in class g3dsys.control.G3DSys
draw() - Method in class g3dsys.images.Axes
draw() - Method in class g3dsys.images.Ball
draw() - Method in class g3dsys.images.Bond
draw() - Method in class g3dsys.images.Box
draw() - Method in class g3dsys.images.Ellipse
draw() - Method in class g3dsys.images.Figure: All Figures know how to draw themselves via override.
draw() - Method in class g3dsys.images.ImageShell
draw() - Method in class g3dsys.images.Line
draw() - Method in class g3dsys.images.Triangle
draw - Static variable in class org.jmol.script.Token
draw(String, String, Point3f, float) - Method in class org.jmol.util.Quaternion
DRAW_BOUNDARY_ALL - Static variable in class etomica.graphics.DisplayCanvas
DRAW_BOUNDARY_MAX - Static variable in class etomica.graphics.DisplayCanvas
DRAW_BOUNDARY_NONE - Static variable in class etomica.graphics.DisplayCanvas
DRAW_BOUNDARY_OUTLINE - Static variable in class etomica.graphics.DisplayCanvas
DRAW_BOUNDARY_SHELL - Static variable in class etomica.graphics.DisplayCanvas
DRAW_EVERY_BOX - Static variable in class g3dsys.images.ImageShell
DRAW_INNER_BOX - Static variable in class g3dsys.images.ImageShell
DRAW_LARGE_BOX - Static variable in class g3dsys.images.ImageShell
Drawable - Interface in etomica.graphics
drawAtom(Graphics, int[], IAtom) - Method in class etomica.graphics.DisplayBoxCanvas2D
drawAtom(Graphics, int[], IAtom) - Method in class etomica.graphics.DisplayBoxSpin2D
drawAtom(Graphics, int[], IAtom) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
drawBond(Point3f, Point3f, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
drawBonds - Variable in class etomica.modules.render.RenderMD.RenderMDParam
drawDashedLine(int, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
drawDottedLine(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
drawEllipse(Point3f, Point3f, Point3f, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawHermite4(int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
drawHermite7(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, short) - Method in class org.jmol.g3d.Graphics3D
drawhover - Static variable in class org.jmol.script.Token
drawImage(Object, Object, int, int, int, int) - Method in interface org.jmol.api.ApiPlatform
drawImage(Object, Object, int, int, int, int) - Method in class org.jmol.awt.Platform
drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawLineAB(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
drawLineList - Variable in class etomica.graphics.DisplayPlot
drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawpicking - Static variable in class org.jmol.script.Token
drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D: draws a rectangle
drawSize - Variable in class etomica.graphics.DisplayBox: Size of drawing region of central image, in pixels
drawSize - Variable in class etomica.graphics.DisplayPolytope: Size of drawing region of central image, in pixels
drawString(String, JmolFont, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D: draws the specified string in the current font.
drawStringNoSlab(String, JmolFont, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D: draws the specified string in the current font.
drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
drawTriangle3C(Point3i, short, Point3i, short, Point3i, short, int) - Method in class org.jmol.g3d.Graphics3D
drawTriangle3I(Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
drB - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
drB - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
drb - Variable in class etomica.potential.P4TorsionDreiding
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHe
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
drbxa - Variable in class etomica.potential.P4TorsionDreiding
drho - Variable in class etomica.statmech.HardSphereSolid.EOSParams
dri - Variable in class etomica.normalmode.PotentialCalculationEFSSP
dri - Variable in class etomica.normalmode.PotentialCalculationLJSP
drij - Variable in class etomica.meam.PotentialCuLREP
drij - Variable in class etomica.meam.PotentialEFS
drij - Variable in class etomica.meam.PotentialFeEAM
drij - Variable in class etomica.models.co2.P2CO2H2OWheatley
drij - Variable in class etomica.models.co2.P2CO2Hellmann
drij - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
drij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
drij - Variable in class etomica.normalmode.PotentialCalculationLJSP
drijRot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
drijRot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
drijRot - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
drijRot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
drijRot - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
drik - Variable in class etomica.meam.PotentialCuLREP
drik - Variable in class etomica.meam.PotentialEFS
drik - Variable in class etomica.meam.PotentialFeEAM
drivePH() - Method in class etomica.integrator.IntegratorGear4NPH
drivePT() - Method in class etomica.integrator.IntegratorGear4NPH
drj - Variable in class etomica.normalmode.P1ConstraintNbr
drj - Variable in class etomica.normalmode.P1ConstraintNbrHcp
drj - Variable in class etomica.normalmode.PotentialCalculationEFSSP
drj - Variable in class etomica.normalmode.PotentialCalculationLJSP
drj_tmp - Variable in class etomica.normalmode.PotentialCalculationLJSP
drjk - Variable in class etomica.meam.PotentialCuLREP
drjk - Variable in class etomica.meam.PotentialEFS
drjk - Variable in class etomica.meam.PotentialFeEAM
drk - Variable in class etomica.normalmode.P1ConstraintNbr
drk - Variable in class etomica.normalmode.P1ConstraintNbrHcp
drLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
drLatTmp - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
drOld - Variable in class etomica.integrator.IntegratorVelocityVerletShake
drOO - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
drop(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
Droplet - Class in etomica.modules.droplet: Mesoscale simulation for Droplet module.
Droplet(Space) - Constructor for class etomica.modules.droplet.Droplet
DropletAtomic - Class in etomica.modules.droplet: Atomic simulation for Droplet module.
DropletAtomic(Space) - Constructor for class etomica.modules.droplet.DropletAtomic
DropletAtomicGraphic - Class in etomica.modules.droplet: Graphic UI for Droplet module.
DropletAtomicGraphic(DropletAtomic, Space) - Constructor for class etomica.modules.droplet.DropletAtomicGraphic
DropletAtomicGraphic.Applet - Class in etomica.modules.droplet
DropletAtomicGraphic.DataSourceVaporDensity - Class in etomica.modules.droplet
DropletGraphic - Class in etomica.modules.droplet: Graphic UI for Droplet module.
DropletGraphic(Droplet, Space) - Constructor for class etomica.modules.droplet.DropletGraphic
DropletGraphic.Applet - Class in etomica.modules.droplet
DropletGraphic.DataProcessorTensorSplitter - Class in etomica.modules.droplet: Inner class to find the total pressure of the system from the pressure tensor.
DropletGraphic.ModifierBoxSize - Class in etomica.modules.droplet
DropOrphanNodes - Class in etomica.graph.operations
DropOrphanNodes() - Constructor for class etomica.graph.operations.DropOrphanNodes
dropPrime() - Method in class etomica.veos.bigdecimal.Ifactor: Divide through the highest possible power of the highest prime.
dropRadius - Variable in class etomica.modules.droplet.DropletAtomic
drPrev - Variable in class etomica.modules.rheology.IntegratorPolymer
drSite0 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
drSite0 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
drSite1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
drSite1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
drSum - Variable in class etomica.modules.sam.MeterTilt
drSum - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
drSum - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
drSum - Variable in class etomica.normalmode.MeterPlaneSlip
drSum - Variable in class etomica.normalmode.MeterTilt
drSum - Variable in class etomica.normalmode.MeterTiltRotation
drSum - Variable in class etomica.normalmode.MeterTiltRotationHistogram
drSumPlane - Variable in class etomica.normalmode.MeterTiltRotation
drSumSave - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
drtmp - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
drTmp - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
drtmp - Variable in class etomica.meam.PotentialFeEAM_LS
dRtmp - Variable in class etomica.meam.PotentialFeEAM_LS
drTmp - Variable in class etomica.potential.EwaldSummation
drtmp - Variable in class etomica.potential.Potential2SoftSphericalLS
drTot - Variable in class etomica.modules.colloid.MeterEnd2End
drvDamp - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
ds - Variable in class etomica.modules.rheology.IntegratorPolymer
ds - Variable in class etomica.normalmode.MeterSolidMirror
dSigma - Variable in class etomica.normalmode.MeterSolidPropsLJ
dsmr - Variable in class etomica.normalmode.DataSourceAvgPressure2
dss - Variable in class etomica.liquidLJ.LjMd3D.ValueCache
dss - Variable in class etomica.liquidLJ.ValueCache
dsspcalchydrogen - Static variable in class org.jmol.script.Token
dst - Variable in class etomica.graph.view.rasterizer.SVGConverter: Destination image path.
dst - Variable in class etomica.virial.CalcFFT
dsum - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
dsum2 - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
dsvo - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
dsvo - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
dsvo - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
dsvo - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImage
dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
dsvo - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
dsvo - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
dsvo - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
dsvo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
dsvo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
dsvo - Variable in class etomica.normalmode.SimOverlap
dsvo - Variable in class etomica.normalmode.SimOverlapLJ
dsvo - Variable in class etomica.normalmode.SimOverlapLJModule
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphere
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
dsvo - Variable in class etomica.normalmode.SimOverlapSSnxy
dsvo - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
dsvo - Variable in class etomica.virial.simulations.SimulationVirialOverlap
dTheta - Variable in class etomica.dimer.IntegratorDimerMin
dTheta - Variable in class etomica.dimer.IntegratorDimerRT
dTheta - Variable in class etomica.virial.MCMoveClusterAngleBend
dTheta - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
du(double) - Method in class etomica.models.rowley.P2RepRowley: The derivative r*du/dr.
du(double) - Method in class etomica.modules.droplet.P2Cohesion
du(double) - Method in class etomica.potential.P1HydrogenMielke
du(double) - Method in interface etomica.potential.P1IntraMolecular
du(double) - Method in class etomica.potential.P2Anharmonic: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2ArgonAziz1993: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
du(double) - Method in class etomica.potential.P2Dreiding: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2Electrostatic
du(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
du(double) - Method in class etomica.potential.P2Exp6: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2Exp6Buckingham: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2Fene: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
du(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
du(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
du(double) - Method in class etomica.potential.P2Harmonic: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2HePCKLJS: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2HeSimplified: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
du(double) - Method in class etomica.potential.P2Ideal: Returns zero.
du(double) - Method in class etomica.potential.P2LennardJones: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2LennardJonesDreiding: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2LJQ
du(double) - Method in class etomica.potential.P2LJQQ
du(double) - Method in class etomica.potential.P2ModifiedMorse: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2Morse: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2QChemInterpolated: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2SoftSphere: The derivative r*du/dr.
du(double) - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the derivative (r du/dr) of the wrapped potential if the separation is less than the cutoff value
du(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
du(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted
du(double) - Method in class etomica.potential.P2SoftTruncated
du(double) - Method in class etomica.potential.P2WCA: The derivative r*du/dr.
du(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
du(double) - Method in interface etomica.potential.Potential2Soft: The derivative of the pair energy, times the separation r: r du/dr.
du(double) - Method in class etomica.potential.Potential2SoftSpherical: The derivative of the pair energy, times the separation r: r du/dr.
du(double) - Method in class etomica.virial.P1IntraLambda
du(double) - Method in class etomica.yukawa.P2HC2Yukawa
du(double) - Method in class etomica.yukawa.P2Yukawa: r * du/dr method.
dU_est - Variable in class etomica.normalmode.MeterSolidPropsLJ
duCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc: Uses result from integration-by-parts to evaluate integral of r du/dr using integral of u.
dUdcosphi(double) - Method in class etomica.potential.P4BondTorsion
dudkT(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
dUdphi(double) - Method in class etomica.potential.P4BondTorsionOPLS
dudphi(int, double, double) - Static method in class etomica.potential.P4TorsionDreiding
dUdRotA - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
dUdRotB - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
dummyRefCluster - Static variable in class etomica.virial.simulations.VirialN2
dummyTarCluster - Static variable in class etomica.virial.simulations.VirialN2
dumpArray(String, float[][], int, int, int, int) - Static method in class org.jmol.util.ArrayUtil
dumpIntArray(int[], int) - Static method in class org.jmol.util.ArrayUtil
dumpit - Variable in class etomica.overlap.DataOverlap
dumpX - Variable in class etomica.metastable.DataProcessorXY
dUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
dUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
dUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
dUnit - Variable in class etomica.modules.swmd.SwmdGraphic
duWork - Variable in class etomica.models.nitrogen.P2Nitrogen
dv - Variable in class etomica.association.BiasVolume2SiteAceticAcid
dv - Variable in class etomica.association.BiasVolumeAceticAcid
dV - Variable in class etomica.data.meter.MeterProfileByVolume
dv - Variable in class etomica.integrator.IntegratorVelocityVerletRattle
dv - Variable in class etomica.modules.catalysis.P2SquareWellBonding
dv - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
dv - Variable in class etomica.modules.catalysis.P2SquareWellSurface
dv - Variable in class etomica.modules.droplet.P2Cohesion
dv - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
dv - Variable in class etomica.modules.mu.P1MagicWall
dv - Variable in class etomica.modules.mu.P2SquareWellOneSide
dv - Variable in class etomica.potential.P2DoubleWell
dv - Variable in class etomica.potential.P2HardSphere
dv - Variable in class etomica.potential.P2PenetrableSphere
dv - Variable in class etomica.potential.P2PenetrableSquareWell
dv - Variable in class etomica.potential.P2SquareWell
dv - Variable in class etomica.potential.P2SquareWellRobust
dv1 - Variable in class etomica.integrator.IntegratorGear4.Agent
dv2 - Variable in class etomica.integrator.IntegratorGear4.Agent
dv3 - Variable in class etomica.integrator.IntegratorGear4.Agent
dv4 - Variable in class etomica.integrator.IntegratorGear4.Agent
dvo - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
dvOO - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
dXl - Variable in class etomica.dimer.IntegratorDimerRT
dy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
dy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
dy12 - Variable in class etomica.util.numerical.AkimaSplineSmoother
dydx(OdeSolver.Variables) - Method in interface etomica.util.OdeSolver.Rhs
dynamicmeasurements - Static variable in class org.jmol.script.Token
Dyne - Class in etomica.units: The dyne unit of force, equal to 1 g-cm/s^2.

E

E(IVector) - Method in interface etomica.api.IVectorMutable: Sets the components of this vector equal to those of the given vector.
E(double) - Method in interface etomica.api.IVectorMutable: Sets all components of this vector equal to the given value.
E(double[]) - Method in interface etomica.api.IVectorMutable: Sets the components of this vector equal to the corresponding elements of the given array.
E(IData) - Method in interface etomica.data.IData: Deep-copies the data from the given object to this one.
E(double) - Method in interface etomica.data.IData: Equals (=) operation, sets all values in data equal to the given value.
E(IData) - Method in class etomica.data.types.DataDouble: Sets the wrapped double to the value in the given instance.
E(double) - Method in class etomica.data.types.DataDouble: Sets the wrapped double to the given value.
E(IData) - Method in class etomica.data.types.DataDoubleArray: Sets the wrapped array of values to the values in the given instance.
E(double[]) - Method in class etomica.data.types.DataDoubleArray: Copies each value in the given array to the values in the wrapped array.
E(double) - Method in class etomica.data.types.DataDoubleArray: Equals (=) operation.
E(IData) - Method in class etomica.data.types.DataDoubleBDArray: Sets the wrapped array of values to the values in the given instance.
E(BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray: Copies each value in the given array to the values in the wrapped array.
E(double) - Method in class etomica.data.types.DataDoubleBDArray: Equals (=) operation.
E(IData) - Method in class etomica.data.types.DataGroup: Applies the E method to all Data elements held, in a one-to-one correspondence with the elements in the given data group.
E(double) - Method in class etomica.data.types.DataGroup
E(IData) - Method in class etomica.data.types.DataTensor: Copies the elements of the given tensor (wrapped in the Data object) to this vector.
E(double) - Method in class etomica.data.types.DataTensor: Sets all tensor elements to the given value.
E(IData) - Method in class etomica.data.types.DataVector: Copies the elements of the given vector (wrapped in the Data object) to this vector.
E(double) - Method in class etomica.data.types.DataVector: Sets all vector elements to the given value.
E(Plane) - Method in class etomica.math.geometry.Plane: Sets the parameters of this plane to make it equivalent to the given one.
E - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
e - Static variable in class etomica.models.water.P2WaterTIP4P
E - Variable in class etomica.potential.P3AxilrodTeller.MyAgent
E(IOrientation) - Method in interface etomica.space.IOrientation: Copies the given orientation to this one.
E(Tensor) - Method in interface etomica.space.Tensor
E(IVector[]) - Method in interface etomica.space.Tensor: Fills the tensor column-wise with the given vectors.
E(double) - Method in interface etomica.space.Tensor
E(double[][]) - Method in interface etomica.space.Tensor: Sets the tensor elements using the elements of the array.
E(double) - Method in class etomica.space1d.Tensor1D
E(double[][]) - Method in class etomica.space1d.Tensor1D
E(IVector[]) - Method in class etomica.space1d.Tensor1D
E(Tensor) - Method in class etomica.space1d.Tensor1D
E(double[]) - Method in class etomica.space1d.Tensor1D
E(double) - Method in class etomica.space1d.Vector1D
E(double[]) - Method in class etomica.space1d.Vector1D
E(IVector) - Method in class etomica.space1d.Vector1D
E(IOrientation) - Method in class etomica.space2d.Orientation2D
E(Tensor) - Method in class etomica.space2d.Tensor2D
E(IVector[]) - Method in class etomica.space2d.Tensor2D
E(double) - Method in class etomica.space2d.Tensor2D
E(double[]) - Method in class etomica.space2d.Tensor2D
E(double[][]) - Method in class etomica.space2d.Tensor2D
E(IVector) - Method in class etomica.space2d.Vector2D
E(double[]) - Method in class etomica.space2d.Vector2D
E(double) - Method in class etomica.space2d.Vector2D
E(double, double) - Method in class etomica.space2d.Vector2D
E(IOrientation) - Method in class etomica.space3d.Orientation3D
E(IOrientation) - Method in class etomica.space3d.OrientationFull3D
E(Tensor) - Method in class etomica.space3d.Tensor3D
E(IVector[]) - Method in class etomica.space3d.Tensor3D
E(double) - Method in class etomica.space3d.Tensor3D
E(double[]) - Method in class etomica.space3d.Tensor3D
E(double[][]) - Method in class etomica.space3d.Tensor3D
E(IVector) - Method in class etomica.space3d.Vector3D
E(double) - Method in class etomica.space3d.Vector3D
E(double, double, double) - Method in class etomica.space3d.Vector3D
E(double[]) - Method in class etomica.space3d.Vector3D
E(Tensor) - Method in class etomica.spaceNd.TensorND
E(IVector[]) - Method in class etomica.spaceNd.TensorND
E(double) - Method in class etomica.spaceNd.TensorND
E(double[][]) - Method in class etomica.spaceNd.TensorND
E(IVector) - Method in class etomica.spaceNd.VectorND
E(double) - Method in class etomica.spaceNd.VectorND
E(double[]) - Method in class etomica.spaceNd.VectorND
E(double) - Method in class etomica.veos.BigValue: Equals (=) operation.
E(IBigValue) - Method in class etomica.veos.BigValue: Equals (=) operation.
E(double) - Method in interface etomica.veos.IBigValue: Equals (=) operation.
E(IBigValue) - Method in interface etomica.veos.IBigValue: Equals (=) operation.
E(double) - Method in class etomica.veos.MyBigDecimal: Equals (=) operation.
E(IBigValue) - Method in class etomica.veos.MyBigDecimal: Equals (=) operation.
E(CoordinatePairLeafSet) - Method in class etomica.virial.CoordinatePairLeafSet
E(CoordinatePairLeafSet) - Method in class etomica.virial.CoordinatePairMoleculeSet
e - Variable in class g3dsys.images.Line
e0 - Variable in class etomica.dimer.IntegratorDimerMin
E0 - Variable in class etomica.models.water.P2WaterSzalewicz
E0 - Static variable in class etomica.potential.P3HydrogenATM
E1 - Variable in class etomica.models.water.P2WaterSzalewicz
e2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
Ea1Tv1(double, IVector) - Method in interface etomica.api.IVectorMutable: Operation (= a1 * v1); sets the components of this to those of the given vector multiplied by the given constant.
Ea1Tv1(double, IVector) - Method in class etomica.space1d.Vector1D
Ea1Tv1(double, IVector) - Method in class etomica.space2d.Vector2D
Ea1Tv1(double, IVector) - Method in class etomica.space3d.Vector3D
Ea1Tv1(double, IVector) - Method in class etomica.spaceNd.VectorND
EAST - Static variable in class etomica.util.Constants.CompassDirection
eBond - Variable in class etomica.graph.operations.ReeHoover.ReeHooverParameters
eBond - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
eBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
eBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
eBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
eBond - Variable in class etomica.virial.cluster.VirialDiagrams
eBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
eBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
eBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
eBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
eBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
eBond - Variable in class etomica.virial.PYGenerator.IteratorEF
Ec - Variable in class etomica.meam.ParameterSetMEAM
Echarge - Static variable in class etomica.models.nitrogen.ConformationNitrogen
Echarge - Static variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
Echarge - Static variable in class etomica.models.water.ConformationWaterGCPMCOM
Echarge - Static variable in class etomica.models.water.ConformationWaterTIP4P
Echarge - Static variable in class etomica.paracetamol.SpeciesParacetamol
Echarge - Static variable in class etomica.virial.ConformationCO2
echo - Static variable in class org.jmol.script.Token
eck_rad_tst(IVectorMutable[]) - Method in class etomica.potential.P2WaterPotentialsJankowski
eCliqueCount - Variable in class etomica.virial.ClusterSumHS
eCliqueCount - Variable in class etomica.virial.ClusterWheatleyHS
eCliqueCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
eCliqueList - Variable in class etomica.virial.ClusterSumHS
eCliqueList - Variable in class etomica.virial.ClusterWheatleyHS
eCliqueList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
Edge - Interface in etomica.graph.model
edgeColor() - Method in class etomica.graph.operations.SplitParameters
edgeColorPairs - Static variable in class etomica.graph.model.impl.MetadataImpl
edgeCount() - Method in interface etomica.graph.model.Graph
edgeCount() - Method in class etomica.graph.model.impl.GraphImpl
edgeCount - Variable in class etomica.virial.ClusterSumHS
edgeCount - Variable in class etomica.virial.ClusterWheatleyHS
edgeCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
edgeCountCore - Variable in class etomica.virial.ClusterWheatleyExtendSW
edgeCountWell - Variable in class etomica.virial.ClusterWheatleyExtendSW
EdgeImpl - Class in etomica.graph.model.impl
EdgeImpl(byte, char) - Constructor for class etomica.graph.model.impl.EdgeImpl
EdgelessIterator - Class in etomica.graph.iterators
EdgelessIterator(Map<Character, Byte>, Map<Character, Byte>) - Constructor for class etomica.graph.iterators.EdgelessIterator
edges() - Method in interface etomica.graph.model.Graph
edges() - Method in class etomica.graph.model.impl.GraphImpl
edges - Variable in class etomica.math.geometry.Polygon
edges - Variable in class etomica.math.geometry.Polyhedron
edges - Static variable in class org.jmol.util.BoxInfo
edgesStack - Variable in class etomica.graph.traversal.Biconnected
edgesToString() - Method in interface etomica.graph.model.Graph
edgesToString() - Method in class etomica.graph.model.impl.GraphImpl
edgeVectors - Variable in class etomica.space.BoundaryRectangular
edgeVertexes - Static variable in class org.jmol.util.TriangleData
EdgeVisitor - Interface in etomica.graph.model
eDrawBondsCB - Variable in class etomica.modules.clustergenerator.MyApplet
edsurlcutoff - Static variable in class org.jmol.script.Token
edsurlformat - Static variable in class org.jmol.script.Token
eExchange - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
efbcBond - Variable in class etomica.virial.cluster.VirialDiagrams
efbcBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
efbcBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
efbcBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
efieldBohrDamped(IVector, IVector[], double) - Method in class etomica.models.water.P2WaterSzalewicz: Calculate the contribution of molecule b to the field on a Use the CC-pol site charges.
efmt - Variable in class etomica.util.ScientificFormat
EFSTungsten - Class in etomica.meam: Molecular-Dynamics Simulation Using the extended Finnis-Sinclair Method (EFS) Potential.
EFSTungsten(int, double, double) - Constructor for class etomica.meam.EFSTungsten
EFSTungsten.Params - Class in etomica.meam
ei - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
ei - Variable in class etomica.potential.PotentialCalculationPhiSum
Eigen - Class in org.jmol.util: Eigenvalues and eigenvectors of a real matrix.
Eigen(int) - Constructor for class org.jmol.util.Eigen
Eigen.EigenSort - Class in org.jmol.util: sort from smallest to largest
EigenSort() - Constructor for class org.jmol.util.Eigen.EigenSort
EigenSystemReduction - Class in etomica.math.linearalgebra
EigenSystemReduction() - Constructor for class etomica.math.linearalgebra.EigenSystemReduction
EigenSystemTriDiagonal - Class in etomica.math.linearalgebra
EigenSystemTriDiagonal() - Constructor for class etomica.math.linearalgebra.EigenSystemTriDiagonal
eigenTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
eigenvalues - Variable in class etomica.normalmode.NormalModes3D
eigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
eigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
eigenvectors - Variable in class etomica.normalmode.MeterHarmonicCoordinate
eigenvectors - Variable in class etomica.normalmode.MeterHarmonicEnergy
eigenvectors - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
eigenVectors - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
eigenvectors - Variable in class etomica.normalmode.NormalModes2D
eigenvectors - Variable in class etomica.normalmode.NormalModes3D
eigenVectors - Variable in class etomica.normalmode.NormalModesVariable
ej - Variable in class etomica.potential.PotentialCalculationPhiSum
ElectricPotential - Class in etomica.units: The dimension for electrostatic potential.
Electron - Class in etomica.units: Unit of charge equal to the magnitude of the charge on an electron.
ElectronVolt - Class in etomica.units: The electronvolt unit of energy, equal to approximately 1.602e-19 Joules.
Electrostatic - Interface in etomica.chem.electrostatics
element - Variable in class etomica.atom.AtomTypeLeaf
Element - Class in etomica.chem.elements: Abstract structure for a class defining an element.
Element(String) - Constructor for class etomica.chem.elements.Element
element - Variable in class etomica.chem.models.ModelChain
element - Static variable in class org.jmol.script.Token
ElementChemical - Class in etomica.chem.elements: Abstract structure for a class defining one of the chemical elements.
ElementChemical(String, double, int) - Constructor for class etomica.chem.elements.ElementChemical
elementDiameterHash - Variable in class etomica.atom.DiameterHashByElement
elementNameFromNumber(int) - Static method in class org.jmol.util.Elements
elementNames - Static variable in class org.jmol.util.Elements
elementNumberFromSymbol(String, boolean) - Static method in class org.jmol.util.Elements
elementNumberMax - Static variable in class org.jmol.util.Elements: one larger than the last elementNumber, same as elementSymbols.length
Elements - Class in org.jmol.util
Elements() - Constructor for class org.jmol.util.Elements
ElementSimple - Class in etomica.chem.elements
ElementSimple(Simulation) - Constructor for class etomica.chem.elements.ElementSimple
ElementSimple(String) - Constructor for class etomica.chem.elements.ElementSimple
ElementSimple(String, double) - Constructor for class etomica.chem.elements.ElementSimple
elementSymbolFromNumber(int) - Static method in class org.jmol.util.Elements
elementSymbols - Static variable in class org.jmol.util.Elements: The default elementSymbols.
elemisono - Static variable in class org.jmol.script.Token
elemno - Static variable in class org.jmol.script.Token
ellipse - Variable in class etomica.modules.droplet.DropletGraphic
ellipse - Variable in class etomica.modules.droplet.EllipseDisplayAction
Ellipse - Class in g3dsys.images: Class for drawing ellipses
Ellipse(G3DSys, short, float, float, float, float) - Constructor for class g3dsys.images.Ellipse
Ellipse(G3DSys, short, Point3f, float, float) - Constructor for class g3dsys.images.Ellipse
Ellipse3D - Class in g3dsys.images: Implements ellipse drawing/filling routines, based on Circl3D
Ellipse3D(Graphics3D) - Constructor for class g3dsys.images.Ellipse3D
EllipseDisplayAction - Class in etomica.modules.droplet
EllipseDisplayAction(SimulationGraphic, float) - Constructor for class etomica.modules.droplet.EllipseDisplayAction
ellipsoid - Static variable in class org.jmol.script.Token
ellipsoidarcs - Static variable in class org.jmol.script.Token
ellipsoidaxes - Static variable in class org.jmol.script.Token
ellipsoidaxisdiameter - Static variable in class org.jmol.script.Token
ellipsoidball - Static variable in class org.jmol.script.Token
ellipsoiddotcount - Static variable in class org.jmol.script.Token
ellipsoiddots - Static variable in class org.jmol.script.Token
ellipsoidfill - Static variable in class org.jmol.script.Token
ellipsoidShades - Static variable in class org.jmol.util.Shader
elong - Variable in class etomica.potential.P2HydrogenPatkowski
elong - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
EMBEDDED_SCRIPT_TAG - Static variable in class org.jmol.viewer.JmolConstants
embeddedSpace - Variable in class etomica.math.geometry.Polytope
embedScript(String) - Static method in class org.jmol.viewer.JmolConstants
eMin - Variable in class etomica.dimer.IntegratorDimerMin
eMon - Variable in class etomica.potential.P2WaterPotentialsJankowski
EMPTY - Static variable in class etomica.graph.model.BitmapFactory
emptySet - Static variable in class org.jmol.util.BitSetUtil
emulEnergyUnit - Static variable in class etomica.potential.PotentialEmul
enabled - Variable in class etomica.modules.sam.SamGraphic.ActionMoveWall
enabled - Variable in class etomica.potential.PotentialGroup.PotentialLinker
enabled - Variable in class etomica.potential.PotentialMaster
enabled - Variable in class etomica.potential.PotentialMaster.PotentialLinker
enabled - Variable in class etomica.potential.PotentialMasterLrc
enableDimerSearch(String, long, Boolean, Boolean) - Method in class etomica.dimer.SimDimerLJadatom
enableDimerSearch(String, long, Boolean, Boolean) - Method in class etomica.dimer.SimDimerMEAMadatom
enableDimerSearch(String, long, Boolean, Boolean) - Method in class etomica.dimer.SimDimerMEAMGB
enableDimerSearch(String, long) - Method in class etomica.kmc.SimKMCLJadatom
enableDimerSearch(String, long) - Method in class etomica.kmc.SimKMCMEAMadatom
enableMinimumSearch(String, Boolean) - Method in class etomica.dimer.SimDimerLJadatom
enableMinimumSearch(String, Boolean) - Method in class etomica.dimer.SimDimerMEAMadatom
enableMinimumSearch(String, Boolean) - Method in class etomica.dimer.SimDimerMEAMGB
enableMolecularDynamics(long) - Method in class etomica.dimer.SimDimerLJadatom
enableMolecularDynamics(long) - Method in class etomica.dimer.SimDimerMEAMadatom
enableMolecularDynamics(long) - Method in class etomica.dimer.SimDimerMEAMGB
enablePBC - Variable in class etomica.models.nitrogen.P2Nitrogen
enableRawLogStatistics() - Method in class etomica.data.AccumulatorAverageCollapsingLog
encapsulateData(String, Object, int) - Static method in class org.jmol.util.Escape
end - Variable in class g3dsys.images.Line
END_ACTION - Static variable in class etomica.action.activity.ControllerEvent
END_URGENT_ACTION - Static variable in class etomica.action.activity.ControllerEvent
ENDCAPS_FLAT - Static variable in class org.jmol.util.GData
ENDCAPS_NONE - Static variable in class org.jmol.util.GData
ENDCAPS_OPEN - Static variable in class org.jmol.util.GData
ENDCAPS_OPENEND - Static variable in class org.jmol.util.GData
ENDCAPS_SPHERICAL - Static variable in class org.jmol.util.GData
endRendering() - Method in class org.jmol.g3d.Graphics3D
endRendering() - Method in class org.jmol.util.GData
energy(IAtomList) - Method in interface etomica.api.IPotentialAtomic: Returns the interaction energy between the given atoms.
energy(IMoleculeList) - Method in interface etomica.api.IPotentialMolecular: Returns the interaction energy between the given atoms.
energy - Variable in class etomica.data.meter.MeterPotentialEnergy
energy - Variable in class etomica.dimer.IntegratorDimerMin
energy - Variable in class etomica.dimer.IntegratorEnergyMap
energy(IAtomList) - Method in class etomica.dimer.P1LepsHarmonic
energy(IAtomList) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
energy(IAtomList) - Method in class etomica.interfacial.P1Wall
energy - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
energy - Variable in class etomica.liquidLJ.MeterPU
energy(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
energy(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
energy - Variable in class etomica.meam.EFSTungsten
energy - Variable in class etomica.meam.MEAM_3DMDwithGB
energy - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
energy - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
energy - Variable in class etomica.meam.MEAM_MC
energy - Variable in class etomica.meam.MEAMMd3D
energy(IAtomList) - Method in class etomica.meam.PotentialCuLREP
energy(IAtomList) - Method in class etomica.meam.PotentialEFS
energy(IAtomList) - Method in class etomica.meam.PotentialFeEAM
energy(IAtomList) - Method in class etomica.meam.PotentialFeEAM_LS
energy(IAtomList) - Method in class etomica.meam.PotentialMEAM
energy(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
energy(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
energy(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
energy(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
energy(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
energy(IMoleculeList) - Method in class etomica.models.co2.PNCO2GCPM
energy(IMoleculeList) - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
energy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM
energy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
energy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
energy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
energy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
energy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
energy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
energy(IMoleculeList) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
energy(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
energy(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenAB
energy(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenAnisotropic
energy(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
energy(IMoleculeList) - Method in class etomica.models.nitrogen.PRotConstraint
energy(IMoleculeList) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
energy(IMoleculeList) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
energy(IMoleculeList) - Method in class etomica.models.water.P2HardAssociationGCPMReference
energy(IMoleculeList) - Method in class etomica.models.water.P2Water3P
energy(IMoleculeList) - Method in class etomica.models.water.P2Water4P
energy(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
energy(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
energy(IMoleculeList) - Method in class etomica.models.water.P2WaterTIP4PHardCore
energy(IMoleculeList) - Method in class etomica.models.water.PNWaterGCPM
energy(IMoleculeList) - Method in class etomica.models.water.PNWaterGCPMThreeSite
energy(IAtomList) - Method in class etomica.modules.adsorption.P1Wall
energy(IAtomList) - Method in class etomica.modules.colloid.P1Wall
energy(IAtomList) - Method in class etomica.modules.colloid.P2HardSphereMC
energy(IAtomList) - Method in class etomica.modules.colloid.P2SquareWellMonomer
energy(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
energy(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
energy(IAtomList) - Method in class etomica.modules.droplet.P1Smash
energy(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
energy(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
energy(IAtomList) - Method in class etomica.modules.mu.P1MagicWall
energy(IAtomList) - Method in class etomica.modules.mu.P2SquareWellOneSide
energy(IAtomList) - Method in class etomica.modules.osmosis.P1HardWall
energy(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
energy(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
energy(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
energy(IAtomList) - Method in class etomica.normalmode.P1Constraint
energy(IAtomList) - Method in class etomica.normalmode.P1ConstraintNbr: Returns sum of energy for all triplets containing the given atom
energy(IAtomList) - Method in class etomica.normalmode.P1ConstraintNbrHcp: Returns sum of energy for all triplets containing the given atom
energy(IAtomList) - Method in class etomica.normalmode.P2XOrder: Interaction energy of the pair.
energy(IAtomList) - Method in class etomica.paracetamol.P2ElectrostaticDreiding
energy(IAtomList) - Method in class etomica.potential.EwaldSummation
energy(IAtomList) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
energy(IMoleculeList) - Method in class etomica.potential.EwaldSumMolecules
energy(double[]) - Method in interface etomica.potential.IPotentialAtomicMultibody: Returns the energy for a configuration of atoms having the given pair separations (squared distances).
energy(IMoleculeList) - Method in class etomica.potential.P1ExternalField
energy(IAtomList) - Method in class etomica.potential.P1HardBoundary
energy(IAtomList) - Method in class etomica.potential.P1HardMovingBoundary
energy(IAtomList) - Method in class etomica.potential.P1HardPeriodic: Returns zero.
energy(IAtomList) - Method in class etomica.potential.P1Harmonic
energy(IAtomList) - Method in class etomica.potential.P1HarmonicSite
energy(IAtomList) - Method in class etomica.potential.P1HydrogenMielke.P1HydrogenMielkeAtomic
energy(IAtomList) - Method in class etomica.potential.P1HydrogenMielke.P2HydrogenMielkeAtomic
energy(IAtomList) - Method in class etomica.potential.P1SoftBoundary
energy(IMoleculeList) - Method in class etomica.potential.P22CLJQ
energy(IMoleculeList) - Method in class etomica.potential.P2CO2EMP
energy(IAtomList) - Method in class etomica.potential.P2DiscreteFeynmanHibbs: Energy of the pair as given by the u(double) method
energy(IMoleculeList) - Method in class etomica.potential.P2DLPOLY
energy(IAtomList) - Method in class etomica.potential.P2EffectiveFeynmanHibbs: Energy of the pair as given by the u(double) method
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationCone: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSites: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeOneSite: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeReference: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardAssociationConeSW: Returns the pair potential energy.
energy(IAtomList) - Method in class etomica.potential.P2HardBondedList
energy(IAtomList) - Method in class etomica.potential.P2HardWrapper
energy(IAtomList) - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
energy(IAtomList) - Method in class etomica.potential.P2HePCKLJS.P2HeTI
energy(IAtomList) - Method in class etomica.potential.P2HeSimplified.P2HeQFH
energy(IAtomList) - Method in class etomica.potential.P2HeSimplified.P2HeTI
energy(IMoleculeList) - Method in class etomica.potential.P2HSDipole
energy(IAtomList) - Method in class etomica.potential.P2HydrogenHinde.P2HydrogenHindeAtomic
energy(IMoleculeList) - Method in class etomica.potential.P2HydrogenHinde.P2HydrogenHindeMolecular
energy(IAtomList) - Method in class etomica.potential.P2HydrogenHindeAtomic
energy(IAtomList) - Method in class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic
energy(IMoleculeList) - Method in class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular
energy(IAtomList) - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
energy(IAtomList) - Method in class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic
energy(IMoleculeList) - Method in class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular
energy(IAtomList) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
energy(IAtomList) - Method in class etomica.potential.P2Ideal: Returns zero.
energy(IMoleculeList) - Method in class etomica.potential.P2LJDipole
energy(IAtomList) - Method in class etomica.potential.P2LJQ
energy(IMoleculeList) - Method in class etomica.potential.P2MoleculeMonatomic
energy(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
energy(IMoleculeList) - Method in class etomica.potential.P2MoleculeTruncated
energy(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
energy(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
energy(IAtomList) - Method in class etomica.potential.P2O2Bartolomei
energy(IAtomList) - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
energy(IMoleculeList) - Method in class etomica.potential.P2QChem
energy(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
energy(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
energy(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
energy(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
energy(IAtomList) - Method in class etomica.potential.P2SemiclassicalAtomic
energy(IMoleculeList) - Method in class etomica.potential.P2SemiclassicalMolecular
energy(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
energy(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
energy(IAtomList) - Method in class etomica.potential.P2SoftTruncated: Returns the energy of the wrapped potential if the separation is less than the cutoff value
energy(IAtomList) - Method in class etomica.potential.P2SpheroPolyhedron
energy(IAtomList) - Method in class etomica.potential.P2TriangleWell
energy(IAtomList) - Method in class etomica.potential.P2WaterPotentialsJankowski
energy(IAtomList) - Method in class etomica.potential.P3AxilrodTeller
energy(IAtomList) - Method in class etomica.potential.P3BondAngle
energy(IAtomList) - Method in class etomica.potential.P3BondAngleDreiding
energy(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHe
energy(double[]) - Method in class etomica.potential.P3CPSNonAdditiveHe
energy(double, double, double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
energy(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
energy(double[]) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
energy(double, double, double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
energy(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
energy(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
energy(double[]) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
energy(double, double, double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
energy(IAtomList) - Method in class etomica.potential.P3HydrogenATM.P3HydrogenAtomic
energy(IMoleculeList) - Method in class etomica.potential.P3HydrogenGarberoglioMolecular
energy(IMoleculeList) - Method in class etomica.potential.P3HydrogenManzhos.P3HydrogenManzhosMolecular
energy(IAtomList) - Method in class etomica.potential.P3Induction
energy(IAtomList) - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
energy(IAtomList) - Method in class etomica.potential.P4BondTorsion
energy(IAtomList) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
energy(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
energy(IAtomList) - Method in class etomica.potential.Potential: Returns the interaction energy between the given atoms.
energy(IAtomList) - Method in class etomica.potential.Potential2HardSpherical: Energy of the pair as given by the u(double) method, with application of any PotentialTruncation that may be defined for the potential.
energy(IAtomList) - Method in class etomica.potential.Potential2SoftSpherical: Energy of the pair as given by the u(double) method
energy(IAtomList) - Method in class etomica.potential.Potential2SoftSphericalLS
energy(IAtomList) - Method in class etomica.potential.PotentialAtomicSum
energy(IMoleculeList) - Method in class etomica.potential.PotentialDLPOLY
energy(IMoleculeList) - Method in class etomica.potential.PotentialEmul
energy(IMoleculeList) - Method in class etomica.potential.PotentialGroup
energy(IMoleculeList) - Method in class etomica.potential.PotentialGroupSoft
energy(IMoleculeList) - Method in class etomica.potential.PotentialMolecular: Returns the interaction energy between the given molecules.
energy(IMoleculeList) - Method in class etomica.potential.PotentialMolecularMonatomic
energy(IMoleculeList) - Method in class etomica.potential.PotentialMolecularSum
energy(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
energy - Variable in class etomica.simulation.prototypes.LjMd2D
energy - Variable in class etomica.simulation.prototypes.LjMd3D
energy(IAtomList) - Method in class etomica.spin.P1MagneticField
energy(IAtomList) - Method in class etomica.spin.P2Spin: Returns the energy for the given pair of atoms.
energy - Variable in class etomica.thermointegration.LjMc3D
energy - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
energy(IAtomList) - Method in class etomica.threaded.PotentialThreaded
Energy - Class in etomica.units: Dimension for all energy units.
energy() - Method in class etomica.units.systems.CGS
energy() - Method in class etomica.units.systems.LJ
energy() - Method in class etomica.units.systems.MKS
energy() - Method in class etomica.units.systems.UnitSystem
energy() - Method in class etomica.units.systems.UnitSystem.Sim
energy(IMoleculeList, double[]) - Method in class etomica.virial.MayerFunctionMolecularThreeBody
energy(IMoleculeList, double[]) - Method in class etomica.virial.MayerFunctionSphericalThreeBody
energy(IMoleculeList, double[]) - Method in class etomica.virial.MayerFunctionThreeBody
energy(IAtomList) - Method in class etomica.virial.P1IntraLambda
energy(IAtomList) - Method in class etomica.virial.PotentialCommonAtomic
energy(IMoleculeList) - Method in class etomica.virial.PotentialEmulCached
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroup3PI
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroupPI
energy(IMoleculeList) - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
energy(IMoleculeList) - Method in class etomica.virial.PotentialNonAdditive
energy(int, IMoleculeList) - Method in class etomica.virial.PotentialNonAdditive
energy(IMoleculeList) - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
energy(IAtomList) - Method in class etomica.yukawa.P2HC2Yukawa: Energy of the pair as given by the u(double) method
energyAtAngle(double) - Method in class etomica.potential.P4BondTorsion
energyAtAngle(double) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
energyAtAngle(double) - Method in class etomica.potential.P4BondTorsionOPLS
energyBox0 - Variable in class etomica.dimer.IntegratorDimerMin
energyBox0 - Variable in class etomica.dimer.IntegratorDimerRT
energyBox1 - Variable in class etomica.dimer.IntegratorDimerRT
energyBox2 - Variable in class etomica.dimer.IntegratorDimerRT
energyBoxMin - Variable in class etomica.dimer.IntegratorDimerMin
energyChange() - Method in class etomica.association.MCMoveBiasUB
energyChange() - Method in class etomica.association.MCMoveBiasUBMolecule
energyChange() - Method in class etomica.association.MCMoveDimer
energyChange() - Method in class etomica.association.MCMoveDimerRotate
energyChange() - Method in class etomica.association.MCMoveSmer
energyChange() - Method in class etomica.association.MCMoveSmerRotate
energyChange() - Method in class etomica.association.MCMoveVolumeAssociated
energyChange() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
energyChange() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
energyChange() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
energyChange() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
energyChange(IBox) - Method in class etomica.integrator.mcmove.MCMove: Returns the change in the energy of the given box that results from the trial move.
energyChange() - Method in class etomica.integrator.mcmove.MCMoveAtom
energyChange(IBox) - Method in class etomica.integrator.mcmove.MCMoveBox
energyChange() - Method in class etomica.integrator.mcmove.MCMoveBox
energyChange() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
energyChange() - Method in class etomica.integrator.mcmove.MCMoveDimer
energyChange() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
energyChange() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
energyChange() - Method in class etomica.integrator.mcmove.MCMoveMolecule
energyChange(IBox) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
energyChange() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
energyChange(IBox) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
energyChange() - Method in class etomica.integrator.mcmove.MCMoveVolume
energyChange(IBox) - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
energyChange() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
energyChange() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
energyChange() - Method in class etomica.models.hexane.MCMoveCBMC
energyChange() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
energyChange() - Method in class etomica.models.hexane.MCMoveReptate
energyChange() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
energyChange() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
energyChange() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
energyChange() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
energyChange() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
energyChange() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
energyChange() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
energyChange() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
energyChange() - Method in class etomica.modules.adsorption.P1Wall
energyChange() - Method in class etomica.modules.catalysis.P2SquareWellBonding
energyChange() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
energyChange() - Method in class etomica.modules.catalysis.P2SquareWellSurface
energyChange() - Method in class etomica.modules.colloid.P1Wall
energyChange() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
energyChange() - Method in class etomica.modules.mu.P1MagicWall
energyChange() - Method in class etomica.modules.mu.P2SquareWellOneSide
energyChange() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
energyChange() - Method in class etomica.modules.osmosis.P1HardWall
energyChange() - Method in class etomica.normalmode.MCMoveAtomCoupled
energyChange() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
energyChange() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
energyChange() - Method in class etomica.normalmode.MCMoveAtomSuperBox
energyChange() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
energyChange() - Method in class etomica.normalmode.MCMoveHarmonic
energyChange() - Method in class etomica.normalmode.MCMoveHarmonicStep
energyChange() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
energyChange() - Method in class etomica.normalmode.MCMovePhaseAngle
energyChange() - Method in class etomica.normalmode.MCMoveSingleMode
energyChange() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
energyChange() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
energyChange() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
energyChange() - Method in class etomica.normalmode.MCMoveVolumeSolid
energyChange() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
energyChange() - Method in class etomica.normalmode.MCMoveWV
energyChange() - Method in class etomica.normalmode.P2XOrder
energyChange() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
energyChange() - Method in class etomica.potential.P1HardBoundary
energyChange() - Method in class etomica.potential.P1HardMovingBoundary
energyChange() - Method in class etomica.potential.P1HardPeriodic: Returns zero.
energyChange() - Method in class etomica.potential.P2DoubleWell
energyChange() - Method in class etomica.potential.P2HardAssociation
energyChange() - Method in class etomica.potential.P2HardBond
energyChange() - Method in class etomica.potential.P2HardBondedList
energyChange() - Method in class etomica.potential.P2HardSphere
energyChange() - Method in class etomica.potential.P2HardWrapper
energyChange() - Method in class etomica.potential.P2Ideal: Returns zero.
energyChange() - Method in class etomica.potential.P2PenetrableBond
energyChange() - Method in class etomica.potential.P2PenetrableSphere
energyChange() - Method in class etomica.potential.P2PenetrableSquareWell
energyChange() - Method in class etomica.potential.P2SquareWell
energyChange() - Method in class etomica.potential.P2SquareWellRobust
energyChange() - Method in class etomica.potential.P2Tether
energyChange() - Method in interface etomica.potential.PotentialHard: returns change in potential energy due to the last collision
energyChange() - Method in class etomica.spin.MCMoveSpinFlip
energyChange() - Method in class etomica.virial.MCMoveChangeBondLength
energyChange() - Method in class etomica.virial.MCMoveClusterAngleBend
energyChange() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
energyChange() - Method in class etomica.virial.MCMoveClusterAtomQ
energyChange(IBox) - Method in class etomica.virial.MCMoveClusterAtomQ
energyChange() - Method in class etomica.virial.MCMoveClusterDiagram
energyChange() - Method in class etomica.virial.MCMoveClusterReptateMulti
energyChange() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
energyChange() - Method in class etomica.virial.MCMoveClusterRingRegrow
energyChange() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
energyChange() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
energyChange() - Method in class etomica.virial.MCMoveClusterRingScale
energyChange(IBox) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
energyEvenLater - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
energyi(IAtom) - Method in class etomica.normalmode.P1ConstraintNbr: Returns the energy for atom i due to requirements for i and its neighbors (but not for i as a neighbor)
energyi(IAtom) - Method in class etomica.normalmode.P1ConstraintNbrHcp: Returns the energy for atom i due to requirements for i and its neighbors (but not for i as a neighbor)
energyij(IAtom, IAtom) - Method in class etomica.normalmode.P1ConstraintNbr: Return the energy for i due to requirement that it be between j and the atom opposite from j.
EnergyMap - Class in etomica.dimer: Simulation class using IntegratorEnergyMap.
EnergyMap(double, String) - Constructor for class etomica.dimer.EnergyMap
EnergyMapCluster - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
EnergyMapCluster(Space) - Constructor for class etomica.dimer.EnergyMapCluster
energyMeter - Variable in class etomica.association.MCMoveDimer
energyMeter - Variable in class etomica.association.MCMoveDimerRotate
energyMeter - Variable in class etomica.association.MCMoveSmer
energyMeter - Variable in class etomica.association.MCMoveSmerRotate
energyMeter - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
energyMeter - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
energyMeter - Variable in class etomica.integrator.mcmove.MCMoveAtom
energyMeter - Variable in class etomica.integrator.mcmove.MCMoveDimer
energyMeter - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
energyMeter - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
energyMeter - Variable in class etomica.integrator.mcmove.MCMoveMolecule
energyMeter - Variable in class etomica.integrator.mcmove.MCMoveVolume
energyMeter - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
energyMeter - Variable in class etomica.models.hexane.MCMoveReptate
energyMeter - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
energyMeter - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
energyMeter - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
energyMeter - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
energyMeter - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
energyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupled
energyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
energyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
energyMeter - Variable in class etomica.normalmode.MCMoveAtomSuperBox
energyMeter - Variable in class etomica.normalmode.MCMoveHarmonicStep
energyMeter - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
energyMeter - Variable in class etomica.normalmode.MCMoveSingleMode
energyMeter - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
energyMeter - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
energyMeter - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
energyMeter - Variable in class etomica.spin.MCMoveSpinFlip
energyMeter - Variable in class etomica.virial.MCMoveClusterAngleBend
energyMeter - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
energyMeter - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
energyMeter - Variable in class etomica.virial.MCMoveClusterRingScale
energyMeter - Variable in class etomica.virial.MCMoveClusterRotateCH3
energyMeter - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
energyMeter - Variable in class etomica.virial.MCMoveClusterTorsionMulti
energyMeter - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
energyMeter - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
energyMeter - Variable in class etomica.virial.MCMoveClusterWiggleMulti
energyNew - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
energyNew - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
energyNew - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
energyNew - Variable in class etomica.normalmode.MCMoveHarmonicStep
energyNew - Variable in class etomica.normalmode.MCMoveSingleMode
energyOld - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
energyOld - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
energyOld - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
energyOld - Variable in class etomica.normalmode.MCMoveHarmonicStep
energyOld - Variable in class etomica.normalmode.MCMoveSingleMode
energySum - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
energySum - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
energySum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
energySum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
energyunits - Static variable in class org.jmol.script.Token
energyVirialCut(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
energyVirialCut(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
energyVirialCut(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
EnsembleToggler(IntegratorGear4NPH, int) - Constructor for class etomica.integrator.IntegratorGear4NPH.EnsembleToggler
EnsembleToggler() - Constructor for class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
ensureCapacity(int) - Method in class etomica.atom.AtomArrayList
ensureCapacity(int) - Method in class etomica.atom.MoleculeArrayList
ensureCapacity(int) - Method in class etomica.util.ObjectArrayList: Increases the capacity of this ArrayList instance, if necessary, to ensure that it can hold at least the number of elements specified by the minimum capacity argument.
ensureHappyIntArrayList() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Refills inArrayList if it's empty.
ensureLength(Object, int) - Static method in class org.jmol.util.ArrayUtil: Very important that this not be used with Int32Array or Float32Array, because it is not initialized to all zeros in MSIE 9.
ensureLengthA(float[], int) - Static method in class org.jmol.util.ArrayUtil
ensureLengthByte(byte[], int) - Static method in class org.jmol.util.ArrayUtil
ensureLengthI(int[], int) - Static method in class org.jmol.util.ArrayUtil
ensureLengthS(String[], int) - Static method in class org.jmol.util.ArrayUtil
ensureLengthShort(short[], int) - Static method in class org.jmol.util.ArrayUtil
ensureOffScreen() - Method in class etomica.graphics.DisplayCanvas
EntropyLottery - Class in etomica.modules.entropylottery
EntropyLottery(Space) - Constructor for class etomica.modules.entropylottery.EntropyLottery
EntropyLotteryGraphic - Class in etomica.modules.entropylottery
EntropyLotteryGraphic(EntropyLottery, Space) - Constructor for class etomica.modules.entropylottery.EntropyLotteryGraphic
EntropyLotteryGraphic.Applet - Class in etomica.modules.entropylottery
EntropyProcessor - Class in etomica.modules.entropylottery: Calculates the entropy of an incoming probability density using Stirling's approximation.
EntropyProcessor() - Constructor for class etomica.modules.entropylottery.EntropyProcessor
EnumeratedType - Class in etomica.util: EnumeratedType classes are used to define a fixed set of specific values that can be taken by a field.
EnumeratedType(String) - Constructor for class etomica.util.EnumeratedType
EnumPalette - Enum in org.jmol.constant: Enum for animation mode.
EnumPotentialParamDescription - Enum in etomica.virial.GUI.models
EnumSiteName - Enum in etomica.virial.GUI.models
EnumStereoMode - Enum in org.jmol.constant
EnumVdw - Enum in org.jmol.constant
Environment - Interface in etomica.graph.engine
EnvironmentImpl - Class in etomica.graph.engine.impl
EnvironmentImpl() - Constructor for class etomica.graph.engine.impl.EnvironmentImpl
eos - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
eos - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
eos - Variable in class etomica.modules.adsorption.ModifierPMu
EOSParams() - Constructor for class etomica.statmech.HardSphereSolid.EOSParams
EOSSW - Class in etomica.modules.adsorption
EOSSW() - Constructor for class etomica.modules.adsorption.EOSSW
EOSSWPatel - Class in etomica.modules.adsorption: EOS for square-well fluids as described by "Generalized equation of state for square-well potentials of variable range" B.
EOSSWPatel() - Constructor for class etomica.modules.adsorption.EOSSWPatel
Ep - Variable in class etomica.models.co2.PNCO2GCPM
Ep - Variable in class etomica.models.co2.PNGCPM
ePlot - Variable in class etomica.zeolite.ZeoliteSimulation
epom - Variable in class etomica.models.water.P2WaterSzalewicz
eps - Variable in class etomica.meam.PotentialFeEAM
epsBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
epsBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
epsBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
epsBox - Variable in class etomica.modules.swmd.SwmdGraphic
epsFactor - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
epsFactor - Variable in class etomica.liquidLJ.MeterWidomInsertionP
epsFe - Variable in class etomica.meam.PotentialFeEAM_LS
epsilon - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
epsilon - Variable in class etomica.math.geometry.Plane: Tolerance used to judge if a given point is in the plane.
epsilon - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
epsilon - Variable in class etomica.models.water.P2Water3P
epsilon - Variable in class etomica.models.water.P2Water4P
epsilon - Variable in class etomica.models.water.P2WaterTIP4PHardCore
epsilon - Variable in class etomica.models.water.PNWaterGCPM
epsilon - Variable in class etomica.modules.adsorption.EOSSW
epsilon - Variable in class etomica.modules.adsorption.P1Wall
epsilon - Variable in class etomica.modules.catalysis.P2SquareWellBonding
epsilon - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
epsilon - Variable in class etomica.modules.catalysis.P2SquareWellSurface
epsilon - Variable in class etomica.modules.colloid.P1Wall
epsilon - Variable in class etomica.modules.dcvgcmd.P1WCAWall
epsilon - Variable in class etomica.modules.droplet.P2Cohesion
epsilon - Variable in class etomica.modules.mu.P2SquareWellOneSide
epsilon - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
epsilon - Variable in class etomica.modules.render.RenderMD.RenderMDParam
epsilon - Variable in class etomica.modules.rosmosis.P1Tether
epsilon - Variable in class etomica.modules.sam.P1WCAWall
epsilon - Variable in class etomica.modules.swmd.SwmdGraphic
epsilon - Variable in class etomica.modules.vle.VLESim
epsilon - Variable in class etomica.normalmode.SoftSphereSolidEOS
epsilon - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
epsilon - Variable in class etomica.potential.P2PenetrableSphere
epsilon - Variable in class etomica.potential.P2PenetrableSquareWell
epsilon - Variable in class etomica.potential.P2ReactionFieldDipole
epsilon - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
epsilon - Variable in class etomica.potential.P2SquareWell
epsilon - Variable in class etomica.potential.P2SquareWellRobust
epsilon - Variable in class etomica.potential.P3BondAngle
epsilon - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
epsilon - Variable in class etomica.units.systems.LJ
epsilon - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
epsilon - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
epsilon - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
epsilon - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
epsilon1 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
epsilon2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
epsilon4 - Variable in class etomica.models.water.P2Water3P
epsilon4 - Variable in class etomica.models.water.P2Water4P
epsilon4 - Variable in class etomica.models.water.P2WaterTIP4PHardCore
epsilon48 - Variable in class etomica.models.water.P2Water3PSoft
epsilon48 - Variable in class etomica.models.water.P2Water4PSoft
EPSILON_0 - Static variable in class etomica.util.Constants: The permittivity of a vacuum, in (sim units) (electron charge)^2.
epsilonAll - Variable in class etomica.models.co2.PNCO2GCPM
epsilonBarrier - Variable in class etomica.modules.catalysis.P2SquareWellBonding
epsilonBarrier - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
epsilonBonding - Variable in class etomica.modules.catalysis.P2SquareWellBonding
epsilonBonding - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
epsilonC - Variable in class etomica.models.co2.PNCO2GCPM
epsilonC - Variable in class etomica.potential.P2CO2EMP
epsilonCG - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
epsilonCO - Variable in class etomica.potential.P2CO2EMP
epsilonCore - Variable in class etomica.modules.render.RenderMD.RenderMDParam
epsilonCore - Variable in class etomica.potential.P2DoubleWell
epsilonCore - Variable in class etomica.potential.P2PenetrableSquareWell
epsilonLJ - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
epsilonLJ - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
epsilonLJ - Variable in class etomica.dielectric.TIP4P_NVT
epsilonMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
epsilonN - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
epsilonNR - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
epsilonO - Variable in class etomica.models.co2.PNCO2GCPM
epsilonO - Variable in class etomica.potential.P2CO2EMP
epsilonSF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
epsilonSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
epsilonSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
epsilonSq - Variable in class etomica.modules.droplet.P2Cohesion
epsilonWell - Variable in class etomica.potential.P2DoubleWell
epsilonWF - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
epsilonWF - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
epsWallWall - Variable in class etomica.modules.colloid.ColloidSim
eq(Matrix) - Method in class etomica.math.linearalgebra.Matrix
Eq - Variable in class etomica.models.co2.PNCO2GCPM
Eq - Variable in class etomica.models.co2.PNGCPM
Eq - Variable in class etomica.models.water.PNWaterGCPM
eqBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
eqBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
eqNumSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
eqPos - Static variable in class etomica.potential.P3HydrogenManzhos
eqSteps - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
eqSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
eqSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
eqSteps - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
eqSteps - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
equalLists(AtomArrayList, AtomArrayList) - Method in class etomica.association.ColorSchemeSmer
equals(IVector) - Method in interface etomica.api.IVector: Returns true if all corresponding elements of this and the given vector are equal; returns false otherwise.
equals(Object) - Method in class etomica.atom.AtomPair
equals(Object) - Method in class etomica.graph.model.impl.AbstractBitmap
equals(Object) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1) for an instance of BitmapOfLong.
equals(Object) - Method in class etomica.graph.model.impl.BitmapOfLongVector
equals(Object) - Method in class etomica.graph.model.impl.EdgeImpl
equals(Object) - Method in class etomica.graph.model.impl.GraphImpl
equals(Object) - Method in class etomica.graph.model.impl.NodeImpl
equals(Object) - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
equals(Object) - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
equals(IVector) - Method in class etomica.space1d.Vector1D
equals(IVector) - Method in class etomica.space2d.Vector2D
equals(IVector) - Method in class etomica.space3d.Vector3D
equals(IVector) - Method in class etomica.spaceNd.VectorND
equals(Object) - Method in class etomica.units.Dimension: Returns true if the given object is a Dimension instance with the same signature as this.
equals(Object) - Method in class etomica.units.Undefined: Returns true if the given object is the singleton instance of this class.
equals(DoubleRange) - Method in class etomica.util.DoubleRange: Tests for equality of mininum and maximum values of this range with given range
equals(IntegerRange) - Method in class etomica.util.IntegerRange: Tests for equality of mininum and maximum values of this range with given range
equals(Object) - Method in class etomica.util.ScientificFormat
equals(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Comparison of two numbers.
equals(Object) - Method in class etomica.virial.IntSet
equals(Object) - Method in class org.jmol.util.AxisAngle4f: Returns true if the Object o is of type AxisAngle4f and all of the data members of o1 are equal to the corresponding data members in this AxisAngle4f.
equals(Object) - Method in class org.jmol.util.BitSet: Compares this object against the specified object.
equals(Object) - Method in class org.jmol.util.Matrix3f: Returns true if the Object o is of type Matrix3f and all of the data members of t1 are equal to the corresponding data members in this Matrix3f.
equals(Object) - Method in class org.jmol.util.Matrix4f: Returns true if the Object o is of type Matrix4f and all of the data members of t1 are equal to the corresponding data members in this Matrix4f.
equals(Object) - Method in class org.jmol.util.Tuple3f: Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this
equals(Object) - Method in class org.jmol.util.Tuple3i: Returns true if the Object o is of type Tuple3i and all of the data members of t are equal to the corresponding data members in this Tuple3i.
equals(Object) - Method in class org.jmol.util.Tuple4f: Returns true if all of the data members of Object are equal to the corresponding data members in this
equilibrate(String, long) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
equilibrate(long) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
equilibrate(String, long) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
equilibrate(String, int, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
equilibrate(String, long, int) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlap
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapLJ
equilibrate(long) - Method in class etomica.normalmode.SimOverlapModule
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphere
equilibrate(long) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
equilibrate(long) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
equilibrate(String, long) - Method in class etomica.normalmode.SimOverlapSSnxy
equilibrate(long) - Method in class etomica.virial.simulations.SimulationVirial
equilibrate(String, long) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
equilibrate(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
equilibrate(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
EQUILIBRATION - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
EQUILIBRATION - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
eRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
eRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
eRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
erfc(double) - Static method in class etomica.math.SpecialFunctions: consider using org.apache.commons.math3.special.Erf.erfc() this method is substantially faster (~10x - 100x), but only accurate to ~10^-7 Complementary error function, computed using the approximant 7.1.26 of Abramowitz & Stegun.
Erg - Class in etomica.units: The erg unit of energy, equal to 1 dyn-cm or 1 g-cm^2/s^2.
err - Variable in class etomica.overlap.DataOverlap
err2prec(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Convert an absolute error to a precision.
err2prec(double, double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Convert an absolute error to a precision.
err2prec(double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Convert a relative error to a precision.
errFac - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
errFac - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
errMult - Variable in class etomica.potential.P2HePCKLJS
ERROR - Static variable in class etomica.data.AccumulatorAverage
error - Variable in class etomica.data.AccumulatorAverage
error(byte) - Method in class etomica.graph.traversal.AbstractTraversal
ERROR - Static variable in interface etomica.graph.traversal.Traversal
error(String, Object[]) - Method in class etomica.graph.view.rasterizer.Main
error(String) - Method in class org.jmol.util.DefaultLogger
error(String) - Static method in class org.jmol.util.Logger: Writes a log at ERROR level.
error(String) - Method in interface org.jmol.util.LoggerInterface: Writes a log at ERROR level.
ERROR_CANNOT_ACCESS_TRANSCODER - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_CANNOT_COMPUTE_DESTINATION - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_CANNOT_OPEN_OUTPUT_FILE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_CANNOT_OPEN_SOURCE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_CANNOT_READ_SOURCE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_CANNOT_USE_DST_FILE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_ILLEGAL_ARGUMENT - Static variable in class etomica.graph.view.rasterizer.Main: Error when an illegal option value was passed to the app {0} Option {1} Option description
ERROR_INVALID_URL - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource
ERROR_NO_SOURCES_SPECIFIED - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_NOT_ENOUGH_OPTION_VALUES - Static variable in class etomica.graph.view.rasterizer.Main: Error when there are missing option values: {0} Option {1} Option description
ERROR_OUTPUT_NOT_WRITEABLE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_SOURCE_SAME_AS_DESTINATION - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_TRAVERSAL_EDGES - Static variable in interface etomica.graph.traversal.Traversal
ERROR_TRAVERSAL_NODES - Static variable in interface etomica.graph.traversal.Traversal
ERROR_TRAVERSAL_ROOT - Static variable in interface etomica.graph.traversal.Traversal
ERROR_UNABLE_TO_CREATE_OUTPUT_DIR - Static variable in class etomica.graph.view.rasterizer.SVGConverter
ERROR_WHILE_CONVERTING_FILES - Static variable in class etomica.graph.view.rasterizer.Main
ERROR_WHILE_RASTERIZING_FILE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
errorBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
errorCode - Variable in exception etomica.graph.view.rasterizer.SVGConverterException: Error code
errorEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
errorEx(String, Throwable) - Static method in class org.jmol.util.Logger: Writes a log at ERROR level with detail on exception.
errorEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface: Writes a log at ERROR level with detail on exception.
errorInfo - Variable in exception etomica.graph.view.rasterizer.SVGConverterException: Additional information about the error condition
errorStat - Variable in class etomica.virial.overlap.DataVirialOverlap
errt - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
errt - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
errt - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
errt - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
escape() - Method in class org.jmol.script.ScriptVariable
Escape - Class in org.jmol.util
Escape() - Constructor for class org.jmol.util.Escape
escape(Object) - Static method in class org.jmol.util.Escape
escapeAF(Object) - Static method in class org.jmol.util.Escape
escapeAI(Object) - Static method in class org.jmol.util.Escape
escapeAP(Object) - Static method in class org.jmol.util.Escape
escapeBs(BitSet, boolean) - Static method in class org.jmol.util.Escape
escapeColor(int) - Static method in class org.jmol.util.Escape
escapeFloatA(float[], boolean) - Static method in class org.jmol.util.Escape
escapeFloatAA(float[][], boolean) - Static method in class org.jmol.util.Escape
escapeFloatAAA(float[][][], boolean) - Static method in class org.jmol.util.Escape
escapeMap(Map<String, Object>) - Static method in class org.jmol.util.Escape
escapeModelFileNumber(int) - Static method in class org.jmol.util.Escape
escapePt(Tuple3f) - Static method in class org.jmol.util.Escape: must be its own, because of the possibility of being null
escapeStr(String) - Static method in class org.jmol.util.Escape
escapeStrA(String[], boolean) - Static method in class org.jmol.util.Escape
escapeUrl(String) - Static method in class org.jmol.util.Escape
escapeVar(ArrayList<ScriptVariable>) - Static method in class org.jmol.util.Escape
eta - Static variable in class etomica.potential.P2HePCKLJS
eta - Variable in class etomica.simulation.prototypes.HSMD3D.HSMD3DParam
eta - Static variable in class org.jmol.script.Token
etas - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
etas - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
ethanol - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
ethanol - Static variable in class etomica.virial.simulations.VirialTraPPEAlcohol
EthanolPotentialHelper - Class in etomica.models.rowley
EthanolPotentialHelper() - Constructor for class etomica.models.rowley.EthanolPotentialHelper
EthanolRouteParams - Class in etomica.models.rowley
EthanolRouteParams() - Constructor for class etomica.models.rowley.EthanolRouteParams
etomica.action - package etomica.action: Provides interfaces and classes that define elementary actions that can be performed on simulation elements.
etomica.action.activity - package etomica.action.activity: Collects classes that extend etomica.action.Activity, which implements Action and is an abstract class appropriate to encapsulate complex, time-consuming tasks.
etomica.AlkaneEH - package etomica.AlkaneEH
etomica.api - package etomica.api
etomica.association - package etomica.association
etomica.association.AceticAcid - package etomica.association.AceticAcid
etomica.association.GCPMWater - package etomica.association.GCPMWater
etomica.atom - package etomica.atom: Provides classes that define and organize atoms and the information related to them.
etomica.atom.iterator - package etomica.atom.iterator: Provides interfaces and classes for iteration of Atoms.
etomica.box - package etomica.box
etomica.chem.electrostatics - package etomica.chem.electrostatics: Under development; subject to significant change or removal.
etomica.chem.elements - package etomica.chem.elements: Under development; subject to significant change or removal.
etomica.chem.models - package etomica.chem.models: Under development; subject to significant change or removal.
etomica.compatibility - package etomica.compatibility: Provides infrastructure that enables classes to specify restrictions on their use with other classes.
etomica.config - package etomica.config: Provides classes for specifying the arrangement of atoms and molecules in space.
etomica.conjugategradient - package etomica.conjugategradient
etomica.data - package etomica.data: Defines structures that represent, generate, process, and output data from a simulation.
etomica.data.meter - package etomica.data.meter: DataSources that act on a Box.
etomica.data.types - package etomica.data.types: Defines classes that encapsulate various types of data and enable casting between them.
etomica.densityofstate - package etomica.densityofstate
etomica.dielectric - package etomica.dielectric
etomica.dimer - package etomica.dimer
etomica.eigenstuff - package etomica.eigenstuff
etomica.exception - package etomica.exception: Defines exceptions for use in the etomica framework.
etomica.freeenergy.npath - package etomica.freeenergy.npath
etomica.gaussianwork - package etomica.gaussianwork
etomica.graph.engine - package etomica.graph.engine
etomica.graph.engine.impl - package etomica.graph.engine.impl
etomica.graph.isomorphism - package etomica.graph.isomorphism
etomica.graph.iterators - package etomica.graph.iterators
etomica.graph.iterators.filters - package etomica.graph.iterators.filters
etomica.graph.model - package etomica.graph.model
etomica.graph.model.comparators - package etomica.graph.model.comparators
etomica.graph.model.impl - package etomica.graph.model.impl
etomica.graph.operations - package etomica.graph.operations
etomica.graph.property - package etomica.graph.property
etomica.graph.traversal - package etomica.graph.traversal
etomica.graph.util - package etomica.graph.util
etomica.graph.view.rasterizer - package etomica.graph.view.rasterizer
etomica.graph.viewer - package etomica.graph.viewer
etomica.graphics - package etomica.graphics
etomica.integrator - package etomica.integrator: Provides Integrator classes that implement different molecular simulation algorithms.
etomica.integrator.mcmove - package etomica.integrator.mcmove: Defines Monte Carlo trial moves that are used by the IntegratorMC class.
etomica.interfacial - package etomica.interfacial
etomica.kmc - package etomica.kmc
etomica.lattice - package etomica.lattice: Provides classes for defining regular arrays of objects (sites), typically points in space.
etomica.lattice.crystal - package etomica.lattice.crystal: Defines primitives and basis points for construction of various Bravais lattices.
etomica.liquidLJ - package etomica.liquidLJ
etomica.listener - package etomica.listener
etomica.mappedvirial - package etomica.mappedvirial
etomica.math - package etomica.math: Provides classes implementing some selected mathematical utilities.
etomica.math.discrete - package etomica.math.discrete: Defines classes that provide some discrete mathematics utilities, particularly the generation of permutations and combinations.
etomica.math.geometry - package etomica.math.geometry: Provides classes that define points, planes, and geometric shapes.
etomica.math.geometry.coordinate - package etomica.math.geometry.coordinate
etomica.math.linearalgebra - package etomica.math.linearalgebra: Defines classes that provide linear algebra utilities, such as eigensystem analysis and solution of linear algebraic equations.
etomica.meam - package etomica.meam
etomica.metastable - package etomica.metastable
etomica.models.aceticAcid - package etomica.models.aceticAcid
etomica.models.clathrates - package etomica.models.clathrates
etomica.models.co2 - package etomica.models.co2
etomica.models.hexane - package etomica.models.hexane: Under development; subject to significant change or removal.
etomica.models.nitrogen - package etomica.models.nitrogen
etomica.models.oneDHardRods - package etomica.models.oneDHardRods
etomica.models.OPLS - package etomica.models.OPLS
etomica.models.rowley - package etomica.models.rowley
etomica.models.traPPE - package etomica.models.traPPE
etomica.models.water - package etomica.models.water: Under development; subject to significant change or removal.
etomica.modifier - package etomica.modifier: Provides classes that define adapters to permit modification of arbitrary fields in arbitrary classes.
etomica.modules.adsorption - package etomica.modules.adsorption
etomica.modules.catalysis - package etomica.modules.catalysis
etomica.modules.chainequilibrium - package etomica.modules.chainequilibrium
etomica.modules.clustergenerator - package etomica.modules.clustergenerator
etomica.modules.colloid - package etomica.modules.colloid
etomica.modules.crystalviewer - package etomica.modules.crystalviewer
etomica.modules.dcvgcmd - package etomica.modules.dcvgcmd
etomica.modules.droplet - package etomica.modules.droplet
etomica.modules.ensembles - package etomica.modules.ensembles
etomica.modules.entropylottery - package etomica.modules.entropylottery
etomica.modules.insertion - package etomica.modules.insertion
etomica.modules.interfacial - package etomica.modules.interfacial
etomica.modules.joulethomson - package etomica.modules.joulethomson
etomica.modules.ljmd - package etomica.modules.ljmd
etomica.modules.materialfracture - package etomica.modules.materialfracture
etomica.modules.mu - package etomica.modules.mu
etomica.modules.multiharmonic - package etomica.modules.multiharmonic
etomica.modules.multiharmonic.mbar - package etomica.modules.multiharmonic.mbar
etomica.modules.multiharmonic.overlap - package etomica.modules.multiharmonic.overlap
etomica.modules.multiharmonic.umbrella - package etomica.modules.multiharmonic.umbrella
etomica.modules.osmosis - package etomica.modules.osmosis
etomica.modules.pistoncylinder - package etomica.modules.pistoncylinder
etomica.modules.reactionequilibrium - package etomica.modules.reactionequilibrium
etomica.modules.render - package etomica.modules.render
etomica.modules.rheology - package etomica.modules.rheology
etomica.modules.rosmosis - package etomica.modules.rosmosis
etomica.modules.sam - package etomica.modules.sam
etomica.modules.swmd - package etomica.modules.swmd
etomica.modules.vle - package etomica.modules.vle
etomica.nbr - package etomica.nbr: Provides classes that implement neighbor-listing capabilities.
etomica.nbr.cell - package etomica.nbr.cell: Provides classes for organizing boxs into subcells and collecting atoms in them for cell-based neighbor iteration.
etomica.nbr.cell.molecule - package etomica.nbr.cell.molecule: Provides classes for organizing boxs into subcells and collecting atoms in them for cell-based neighbor iteration.
etomica.nbr.list - package etomica.nbr.list: Provides classes that implement neighbor-listing capabilities.
etomica.nbr.list.molecule - package etomica.nbr.list.molecule: Provides classes that implement neighbor-listing capabilities.
etomica.nbr.molecule - package etomica.nbr.molecule: Provides classes that implement neighbor-listing capabilities.
etomica.nbr.site - package etomica.nbr.site
etomica.normalmode - package etomica.normalmode
etomica.normalmode.nptdemo - package etomica.normalmode.nptdemo
etomica.overlap - package etomica.overlap
etomica.paracetamol - package etomica.paracetamol
etomica.parser - package etomica.parser
etomica.potential - package etomica.potential
etomica.rotation - package etomica.rotation
etomica.simulation - package etomica.simulation
etomica.simulation.prototypes - package etomica.simulation.prototypes
etomica.space - package etomica.space: Specifies abstract classes and interfaces that define the nature of the physical space in which a simulation is performed.
etomica.space1d - package etomica.space1d: Implementation of space classes for a 1-dimensional space.
etomica.space2d - package etomica.space2d: Implementation of space classes for a 2-dimensional space.
etomica.space3d - package etomica.space3d: Implementation of space classes for a 3-dimensional space.
etomica.spaceNd - package etomica.spaceNd
etomica.species - package etomica.species
etomica.spin - package etomica.spin
etomica.statmech - package etomica.statmech
etomica.surfacetension - package etomica.surfacetension
etomica.tests - package etomica.tests
etomica.thermointegration - package etomica.thermointegration
etomica.threaded - package etomica.threaded
etomica.threaded.atom - package etomica.threaded.atom
etomica.threaded.domain - package etomica.threaded.domain
etomica.threads - package etomica.threads
etomica.tmmc - package etomica.tmmc
etomica.units - package etomica.units: Defines units and dimensions that are used for conversions during input or output.
etomica.units.systems - package etomica.units.systems: Provides classes that specify a system of units, such as SI, English, etc.
etomica.util - package etomica.util: Collects miscellaneous utility classes that serve a variety of purposes.
etomica.util.numerical - package etomica.util.numerical
etomica.veos - package etomica.veos
etomica.veos.bigdecimal - package etomica.veos.bigdecimal
etomica.virial - package etomica.virial
etomica.virial.cluster - package etomica.virial.cluster
etomica.virial.GUI - package etomica.virial.GUI
etomica.virial.GUI.components - package etomica.virial.GUI.components
etomica.virial.GUI.containers - package etomica.virial.GUI.containers
etomica.virial.GUI.controllers - package etomica.virial.GUI.controllers
etomica.virial.GUI.models - package etomica.virial.GUI.models
etomica.virial.GUI.views - package etomica.virial.GUI.views
etomica.virial.overlap - package etomica.virial.overlap
etomica.virial.paralleltempering - package etomica.virial.paralleltempering
etomica.virial.simulations - package etomica.virial.simulations
etomica.yukawa - package etomica.yukawa
etomica.zeolite - package etomica.zeolite
EtomicaGraphic() - Constructor for class etomica.graphics.AboutBoxWindow.EtomicaGraphic
EtomicaPlot - Class in etomica.graphics: Custom Plot subclass that allows us to sanely reset the axes autoscaling and repaint when a hidden plot is shown (without resetting all plot parameters).
EtomicaPlot(DisplayPlot) - Constructor for class etomica.graphics.EtomicaPlot
EtomicaTheme - Class in etomica.graphics: This class overrides the colors in the DefaultMetalTheme.
EtomicaTheme() - Constructor for class etomica.graphics.EtomicaTheme
Euler - Class in etomica.veos.bigdecimal: Euler numbers
Euler() - Constructor for class etomica.veos.bigdecimal.Euler: Ctor().
EulerPhi - Class in etomica.veos.bigdecimal: Euler totient function.
EulerPhi() - Constructor for class etomica.veos.bigdecimal.EulerPhi: Default constructor.
eUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
eUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
eUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
eUnit - Variable in class etomica.modules.swmd.SwmdGraphic
Ev1Mv2(IVector, IVector) - Method in interface etomica.api.IVectorMutable: Sets the components of this vector equal to (v1 - v2)
Ev1Mv2(IVector, IVector) - Method in class etomica.space1d.Vector1D
Ev1Mv2(IVector, IVector) - Method in class etomica.space2d.Vector2D
Ev1Mv2(IVector, IVector) - Method in class etomica.space3d.Vector3D
Ev1Mv2(IVector, IVector) - Method in class etomica.spaceNd.VectorND
Ev1Pv2(IVector, IVector) - Method in interface etomica.api.IVectorMutable: Sets the components of this vector equal to (v1 + v2)
Ev1Pv2(IVector, IVector) - Method in class etomica.space1d.Vector1D
Ev1Pv2(IVector, IVector) - Method in class etomica.space2d.Vector2D
Ev1Pv2(IVector, IVector) - Method in class etomica.space3d.Vector3D
Ev1Pv2(IVector, IVector) - Method in class etomica.spaceNd.VectorND
Ev1v2(IVector, IVector) - Method in interface etomica.space.Tensor: Sets this equal to the dyadic or outer product of the given vectors.
Ev1v2(IVector, IVector) - Method in class etomica.space1d.Tensor1D
Ev1v2(IVector, IVector) - Method in class etomica.space2d.Tensor2D
Ev1v2(IVector, IVector) - Method in class etomica.space3d.Tensor3D
Ev1v2(IVector, IVector) - Method in class etomica.spaceNd.TensorND
eValNum - Variable in class etomica.normalmode.IntegratorHarmonic
eValPostAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
eValSlider - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
eVec - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
evenN - Variable in class etomica.potential.P2SoftSphere
eventing - Variable in class etomica.integrator.IntegratorEventManager
eventLinker - Variable in class etomica.integrator.IntegratorHard.Agent
eventList - Variable in class etomica.integrator.IntegratorHard
eventManager - Variable in class etomica.integrator.Integrator
eventManager - Variable in class etomica.integrator.IntegratorManagerMC
eventManager - Variable in class etomica.simulation.Simulation
eventManager - Variable in class etomica.space.Boundary
EventManager - Class in etomica.util: Class to take care of listener lists and event firing for simulation elements.
EventManager() - Constructor for class etomica.util.EventManager
EventManager.Linker - Class in etomica.util: Class used to construct a two-way linked list of listeners.
EwaldSummation - Class in etomica.potential: Sabry
EwaldSummation(IBox, AtomLeafAgentManager<EwaldSummation.MyCharge>, ISpace, double, double) - Constructor for class etomica.potential.EwaldSummation
EwaldSummation.MyCharge - Class in etomica.potential
EwaldSummation.P2EwaldReal - Class in etomica.potential
EwaldSumMolecules - Class in etomica.potential: basic Ewald Sum U(coulomb) = U(real-space) + U(fourier-space) + U(self-correction) Frenkel&Smit, p292-300.especially equation(12.1.25) also Allen, computer simulation of liquids Ch5
EwaldSumMolecules(IBox, AtomLeafAgentManager, double, double, Space) - Constructor for class etomica.potential.EwaldSumMolecules
EwaldSumMolecules.MyCharge - Class in etomica.potential
ex - Variable in class etomica.normalmode.MeterSolidPropsLJ
EXA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺¹⁸.
excBond - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
excBond - Variable in class etomica.virial.cluster.VirialDiagrams
excBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
excBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
excBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
ExceptionDoNotRemoveSpecies - Exception in etomica.virial.GUI.components
ExceptionDoNotRemoveSpecies(int) - Constructor for exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
ExceptionSameSpeciesSamePotential - Exception in etomica.virial.GUI.components
ExceptionSameSpeciesSamePotential() - Constructor for exception etomica.virial.GUI.components.ExceptionSameSpeciesSamePotential
ExceptionSingleSiteAtomicPotential - Exception in etomica.virial.GUI.components
ExceptionSingleSiteAtomicPotential() - Constructor for exception etomica.virial.GUI.components.ExceptionSingleSiteAtomicPotential
ExchangeSplit - Class in etomica.virial.cluster: This operation splits each e-bond component into a sum of permuted (exchanged) nodes.
ExchangeSplit() - Constructor for class etomica.virial.cluster.ExchangeSplit
ExchangeSplit.ExchangeSplitParameters - Class in etomica.virial.cluster
ExchangeSplitParameters(MulFlexible.MulFlexibleParameters, byte, char, char, boolean) - Constructor for class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
Exclude - Class in etomica.graph.operations: exclude diagrams having multiple association bond
Exclude() - Constructor for class etomica.graph.operations.Exclude
excludeArticulationPairCB - Variable in class etomica.modules.clustergenerator.MyApplet
excludeArticulationPointCB - Variable in class etomica.modules.clustergenerator.MyApplet
excludeBogusConfigs - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
excludeBogusConfigs - Variable in class etomica.virial.MeterVirialBinMultiThreaded
excludeNodalPointCB - Variable in class etomica.modules.clustergenerator.MyApplet
ExcludeParameters - Class in etomica.graph.operations
ExcludeParameters() - Constructor for class etomica.graph.operations.ExcludeParameters
excludes(IPotential) - Method in class etomica.atom.iterator.IteratorDirective
excludes(IPotential) - Method in class etomica.atom.iterator.IteratorDirective.PotentialCriterion: Definition of criterion.
EXCLUSIVE - Static variable in class etomica.data.DataSourceUniform.LimitType: Limit type indicating that specified limit is not included in the range, and that the extreme value should be one full step from the specified limit.
execPath - Static variable in class etomica.potential.PotentialEmul
execute() - Method in class etomica.graph.view.rasterizer.Main
execute() - Method in class etomica.graph.view.rasterizer.SVGConverter: Starts the conversion process.
executeOnload - Variable in class etomica.graph.view.rasterizer.SVGConverter: Execute the 'onload' scripts flag
exitflag - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
Exp - Class in etomica.graph.operations
Exp() - Constructor for class etomica.graph.operations.Exp
Exp() - Constructor for class etomica.util.Function.Exp
exp(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The exponential function.
exp(MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The base of the natural logarithm.
exp6 - Variable in class etomica.virial.MayerSSSeries
exp_s - Variable in class etomica.potential.EwaldSumMolecules
expandSources(List) - Method in class etomica.graph.view.rasterizer.Main: Scans the input vector and replaces directories with the list of SVG files they contain
expected_result - Variable in class etomica.compatibility.FeatureRequirement
expHi() - Method in class etomica.graph.operations.ExpParameters
expLo() - Method in class etomica.graph.operations.ExpParameters
exponent() - Method in class etomica.graph.operations.PowParameters
exponent - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
exponent - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
exponent - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
exponent(double) - Static method in class etomica.util.Strings: Returns a String that formats the given value as an exponent.
exponent(String) - Static method in class etomica.util.Strings: Returns a String that formats the given String as an exponent.
EXPONENT_FIELD - Static variable in class etomica.util.ScientificFormat
exponential() - Method in class etomica.math.Complex: Complex exponential (doesn't change this Complex number).
exponentN - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
exponentN - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimBennet.SimBennetParam
exponentN - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
exponentN - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
exponentN - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
exponentN - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
EXPORT_CARTESIAN - Static variable in class org.jmol.util.GData
EXPORT_DRIVER_LIST - Static variable in class org.jmol.viewer.JmolConstants
EXPORT_NOT - Static variable in class org.jmol.util.GData
EXPORT_RAYTRACER - Static variable in class org.jmol.util.GData
ExpParameters - Class in etomica.graph.operations
ExpParameters(byte, byte) - Constructor for class etomica.graph.operations.ExpParameters
externalField - Variable in class etomica.potential.P1ExternalField
externalMeter - Variable in class etomica.models.hexane.MCMoveCBMC
ExternalVirialDiagrams - Class in etomica.virial.cluster
ExternalVirialDiagrams(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.ExternalVirialDiagrams
extractData(String, int, int, int) - Static method in class org.jmol.util.Parser
extractQuotedStrings(String) - Static method in class etomica.util.ScientificFormat
extraFile - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
extraTargetClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
ey - Variable in class etomica.util.numerical.AkimaSplineSmoother

F

f(double) - Method in interface etomica.api.IFunction
f(double[]) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
f(double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
f(double[]) - Method in class etomica.conjugategradient.TestFiniteDifferenceDerivative
f(double[]) - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
F - Variable in class etomica.dimer.IntegratorDimerRT
f - Variable in class etomica.graph.operations.SplitOneBiconnected.SplitOneParametersBC
f(double) - Method in class etomica.liquidLJ.LjMd3D.VolumeBias
f(double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
f(int[], double[][]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
f(double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
f - Variable in class etomica.modules.droplet.MeterDeformation
f(double) - Method in class etomica.modules.vle.B2Fit.FunctionB2LJQ
f(double) - Method in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
f(int) - Method in interface etomica.normalmode.CoordinateDefinitionHSDimer.IntegerFunction
f - Variable in class etomica.normalmode.LJVacancyMin.VectorForce
f - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
f - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
f - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
f - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
f(double[]) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
f - Variable in class etomica.potential.P2HydrogenPatkowski
f - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
f(double) - Method in class etomica.potential.P3HydrogenGarberoglioMolecular
f(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
f(double) - Method in class etomica.util.Function.Abs
f(double) - Method in class etomica.util.Function.Chop
f(double) - Method in class etomica.util.Function.Constant
f(double) - Method in class etomica.util.Function.Exp
f(double) - Method in class etomica.util.Function.Identity
f(double) - Method in class etomica.util.Function.Linear
f(double) - Method in class etomica.util.Function.Log
f(double) - Method in class etomica.util.Function.Reciprocal
f(double) - Method in class etomica.util.Function.Sqrt
f(IFunction) - Method in interface etomica.util.Functional
f(double) - Method in class etomica.util.FunctionChain: Calculates function by applying subfunctions, in the ordered they were added.
f(Object) - Method in interface etomica.util.FunctionGeneral: Method that performs the mapping defined by the function.
f(double[]) - Method in interface etomica.util.FunctionMultiDimensional
f - Variable in class etomica.util.Grabber
f(double[]) - Method in class etomica.util.numerical.CalcGradientDifferentiable
f(double[]) - Method in class etomica.util.numerical.FiniteDifferenceDerivative
f(double[], double) - Method in class etomica.util.numerical.FittingFunctionNonLinear
f(double[], double) - Method in class etomica.util.numerical.FittingFunctionNonLinearB
f(double) - Method in class etomica.util.numerical.Function1d
f - Variable in class etomica.util.numerical.NewtonMinimization
f - Variable in class etomica.util.numerical.SteepestDescent
f(double[]) - Method in interface etomica.util.Transform
f(double[]) - Method in class etomica.util.Transform.Fourier
f - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
f - Variable in class etomica.virial.ClusterChainHS
f - Variable in class etomica.virial.ClusterChainSoft
f - Variable in class etomica.virial.ClusterSinglyConnected
f - Variable in class etomica.virial.ClusterSum
f(IMoleculeList, double, double) - Method in class etomica.virial.ClusterSumIC.FR2
f - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
f - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
f - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
f - Variable in class etomica.virial.ClusterTree
f - Variable in class etomica.virial.ClusterWheatleyHS
f - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
f - Variable in class etomica.virial.ClusterWheatleySoft
f - Variable in class etomica.virial.ClusterWheatleySoftBD
f - Variable in class etomica.virial.ConfigurationClusterAceticAcid
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerD2FDT2Spherical
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerDFDTSpherical
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerDFQFHDTSpherical
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerEGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerEHardSphere
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerENonGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerESpherical
f(IMoleculeList, double, double) - Method in interface etomica.virial.MayerFunction: returns Mayer function between atoms in the pair at temperature 1/beta
f(IMoleculeList, double[], double) - Method in interface etomica.virial.MayerFunctionNonAdditive: returns exp(-beta*(U - Upair)) r2 is listed in the order (0,1),(0,2)...(0,n-1),(1,2),(1,3)...(1,n-1)...(n-2,n-1)
f(IMoleculeList, int, int[], double[], double) - Method in interface etomica.virial.MayerFunctionNonAdditive: returns exp(-beta*(U - Upair)) This method allows an implementation to operate on distances and indices instead of molecules.
f(IMoleculeList, double[], double) - Method in class etomica.virial.MayerFunctionNonAdditiveFull: returns exp(-beta*(U - Upair)) r2 is listed in the order (0,1),(0,2)...(0,n-1),(1,2),(1,3)...(1,n-1)...(n-2,n-1)
f(IMoleculeList, int, int[], double[], double) - Method in class etomica.virial.MayerFunctionNonAdditiveFull: returns exp(-beta*(U - Upair)) This method allows an implementation to operate on distances and indices instead of molecules.
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionProductGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionSum
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionSumGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerFunctionTemperature
f(IMoleculeList, double[], double) - Method in class etomica.virial.MayerFunctionThreeBody
f(IMoleculeList, int, int[], double[], double) - Method in class etomica.virial.MayerFunctionThreeBody
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerGeneralAtomic
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerGeneralSpherical
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerHardSphere
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerPTAtt
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerPUGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerSphericalPlus
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerSphericalPTAtt
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerSSSeries
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerWell
f(IMoleculeList, double, double) - Method in class etomica.virial.MayerXSpherical
f(IMoleculeList, double, double) - Method in class etomica.virial.MuFGeneral
f(IMoleculeList, double, double) - Method in class etomica.virial.MuGeneral
F0 - Variable in class etomica.dimer.IntegratorDimerMin
F1 - Variable in class etomica.dimer.IntegratorDimerRT
f1 - Variable in class etomica.normalmode.MeterSolidProps
f1 - Variable in class etomica.normalmode.MeterSolidPropsLJ
f1 - Variable in class etomica.normalmode.PotentialCalculationEFSSP
f1 - Variable in class etomica.normalmode.PotentialCalculationLJSP
f1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
f12 - Variable in class etomica.virial.ClusterSumIC
F1perp - Variable in class etomica.dimer.IntegratorDimerRT
F1star - Variable in class etomica.dimer.IntegratorDimerRT
F2 - Variable in class etomica.dimer.IntegratorDimerRT
f2 - Variable in class etomica.normalmode.MeterSolidProps
f2 - Variable in class etomica.normalmode.MeterSolidPropsLJ
f2 - Variable in class etomica.virial.ConfigurationClusterAceticAcid
F2perp - Variable in class etomica.dimer.IntegratorDimerRT
F2star - Variable in class etomica.dimer.IntegratorDimerRT
f3 - Variable in class etomica.virial.ConfigurationClusterAceticAcid
f6(double) - Method in class etomica.potential.P2NitrogenHellmann
fA - Variable in class etomica.virial.ClusterSumHS
fA - Variable in class etomica.virial.ClusterWheatleyExtendSW
fA - Variable in class etomica.virial.ClusterWheatleyHS
fA - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fA - Variable in class etomica.virial.ClusterWheatleySoft
fA - Variable in class etomica.virial.ClusterWheatleySoftBD
fAB - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fABList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fABValues - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fac - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
fac - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
fac - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
fac - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
fac - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
fac - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
fac - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
fac - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
fac - Variable in class etomica.modules.droplet.P2Cohesion
fac - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
fac - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
fac - Variable in class etomica.potential.P2HePCKLJS.P2HeQFH
fac - Variable in class etomica.potential.P2HePCKLJS.P2HeTI
fac - Variable in class etomica.potential.P2HeSimplified.P2HeQFH
fac - Variable in class etomica.potential.P2HeSimplified.P2HeTI
fac - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
fac - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
fac - Variable in class etomica.potential.P2ReactionFieldDipole
fac - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
fac - Variable in class etomica.potential.P2SemiclassicalAtomic
fac - Variable in class etomica.potential.P2SemiclassicalMolecular
fac - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
fac - Variable in class etomica.virial.MCMoveClusterRingRegrow
fac - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
fac - Variable in class etomica.virial.MCMoveClusterRingScale
fac1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
fac1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
fac10 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
fac2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
fac3 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac4 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac5 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac6 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac7 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac8 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
fac9 - Static variable in class etomica.virial.MCMoveClusterAtomHSRing
faces - Variable in class etomica.math.geometry.Polyhedron
factor - Variable in class etomica.graph.operations.Decorate.DecorateParameters
Factor - Class in etomica.graph.operations: Factor graphs.
Factor() - Constructor for class etomica.graph.operations.Factor
factor() - Method in class etomica.graph.operations.MulScalarParameters
factor(Graph, byte, byte) - Method in class etomica.graph.property.FactorFFT
factOrder - Variable in class etomica.virial.MayerPTAtt
factOrder - Variable in class etomica.virial.MayerSphericalPTAtt
FactorFFT - Class in etomica.graph.property
FactorFFT() - Constructor for class etomica.graph.property.FactorFFT
factorial(int) - Static method in class etomica.math.SpecialFunctions: The factorial function, n!
Factorial - Class in etomica.veos.bigdecimal: Factorials.
Factorial() - Constructor for class etomica.veos.bigdecimal.Factorial: ctor().
FactorOnce - Class in etomica.graph.operations: Factor graphs once.
FactorOnce() - Constructor for class etomica.graph.operations.FactorOnce
FactorOnce.FactorOnceParameters - Class in etomica.graph.operations
FactorOnceParameters(byte, boolean) - Constructor for class etomica.graph.operations.FactorOnce.FactorOnceParameters
factors() - Method in interface etomica.graph.model.Graph: factors are considered to be variables that go with the diagram, such as rhoA^2 rhoB^3 The array contains the exponents on each of the factors
factors() - Method in class etomica.graph.model.impl.GraphImpl
FACTORY - Static variable in class etomica.integrator.mcmove.MCMoveSwapConfiguration
FACTORY - Static variable in class etomica.nbr.cell.Cell
FACTORY - Static variable in class etomica.nbr.cell.molecule.CellMolecular
FACTORY - Static variable in class etomica.nbr.site.AtomSite
FACTORY - Static variable in class etomica.virial.paralleltempering.MCMoveSwapCluster
FAILED - Static variable in class etomica.action.activity.Controller.ActionStatus
fAList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
falseButton() - Method in class etomica.graphics.DeviceToggleRadioButtons
fancyMove - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
fancyMove - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
FastFourierTransform - Class in etomica.util: This utility receives a set of data points, either Real, Imaginary or Both and performs a Discrete Fourier Transform on them using the Fast Fourier Transform algorithm.
FastFourierTransform() - Constructor for class etomica.util.FastFourierTransform: Constructors accepting: nothing; all reals; both real and imaginary
FastFourierTransform(double[]) - Constructor for class etomica.util.FastFourierTransform
FastFourierTransform(double[], double[]) - Constructor for class etomica.util.FastFourierTransform
fastRefresh() - Method in class g3dsys.control.G3DSys: A less thorough redraw for a quick refresh
fatal(String) - Method in class org.jmol.util.DefaultLogger
fatal(String) - Static method in class org.jmol.util.Logger: Writes a log at FATAL level.
fatal(String) - Method in interface org.jmol.util.LoggerInterface: Writes a log at FATAL level.
fatalEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
fatalEx(String, Throwable) - Static method in class org.jmol.util.Logger: Writes a log at FATAL level with detail on exception.
fatalEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface: Writes a log at ERROR level with detail on exception.
fAValues - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fB - Variable in class etomica.virial.ClusterSumHS
fB - Variable in class etomica.virial.ClusterWheatleyExtendSW
fB - Variable in class etomica.virial.ClusterWheatleyHS
fB - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fB - Variable in class etomica.virial.ClusterWheatleySoft
fB - Variable in class etomica.virial.ClusterWheatleySoftBD
fBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
fBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
fBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
fBond - Variable in class etomica.virial.cluster.VirialDiagrams
fBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
fBond - Variable in class etomica.virial.cluster.VirialDiagramsMix2
fBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
fBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
fBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
fBond - Variable in class etomica.virial.PYGenerator.IteratorEF
fC - Variable in class etomica.virial.ClusterSumHS
fC - Variable in class etomica.virial.ClusterWheatleyExtendSW
fC - Variable in class etomica.virial.ClusterWheatleyHS
fC - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fC - Variable in class etomica.virial.ClusterWheatleySoft
fC - Variable in class etomica.virial.ClusterWheatleySoftBD
FCC - Static variable in class etomica.normalmode.SoftSphereSolidEOS
FCC - Static variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
fCList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fct(int) - Method in class etomica.potential.P2HydrogenPatkowski
fct(int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
fct - Variable in class etomica.potential.P2O2Bartolomei
fDrawBondsCB - Variable in class etomica.modules.clustergenerator.MyApplet
fe - Variable in class etomica.normalmode.MeterSolidPropsLJ
fe - Variable in class etomica.normalmode.PotentialCalculationLJSP
Feature - Class in etomica.compatibility: Tentative property-based infrastructure for a general property-based compatibility algorithm
Feature(String) - Constructor for class etomica.compatibility.Feature
FeatureRequirement - Class in etomica.compatibility
FeatureSet - Class in etomica.compatibility: Container for a class features.
FeatureSet() - Constructor for class etomica.compatibility.FeatureSet
fee - Variable in class etomica.normalmode.MeterSolidPropsLJ
fee - Variable in class etomica.normalmode.PotentialCalculationLJSP
Feff - Variable in class etomica.dimer.IntegratorDimerRT
Feffstar - Variable in class etomica.dimer.IntegratorDimerRT
FEMTO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-15.
FerrenbergSwendsen - Class in etomica.densityofstate
FerrenbergSwendsen() - Constructor for class etomica.densityofstate.FerrenbergSwendsen
fExchange - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
ffBond - Variable in class etomica.virial.cluster.VirialDiagrams
ffBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
ffr - Variable in class etomica.virial.CalcFFT
FFTDecomposition - Class in etomica.graph.property: Class that pretends to be a property and determines how to decompose a diagram into parts that can be treated with FFT and others that can not.
FFTDecomposition() - Constructor for class etomica.graph.property.FFTDecomposition
FFTDecomposition.ComparatorStrand - Class in etomica.graph.property: Comparator that recursively compares two strands
fFunction - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
fFunction - Variable in class etomica.util.numerical.FiniteDifferenceDerivative
fid - Variable in class org.jmol.util.JmolFont
field - Variable in class etomica.spin.Heisenberg
fieldE - Variable in class etomica.potential.PotentialCalculationPhiSum
FieldNodeCount - Class in etomica.graph.iterators.filters: Filters by number of field nodes.
FieldNodeCount(GraphIterator, int) - Constructor for class etomica.graph.iterators.filters.FieldNodeCount
FieldNodeCountMax - Class in etomica.graph.property
FieldNodeCountMax(int) - Constructor for class etomica.graph.property.FieldNodeCountMax
fields - Variable in class etomica.util.ParseArgs
fields - Variable in class etomica.util.ReadParameters
Figure - Class in g3dsys.images: Superclass for drawable shapes.
fij - Variable in class etomica.mappedvirial.MeterMeanForce
file - Variable in class etomica.dimer.IntegratorDimerMin
file - Variable in class etomica.dimer.IntegratorDimerRT
file - Variable in class etomica.modules.render.RenderMD.RenderMDParam
file - Variable in class etomica.potential.P2HydrogenPatkowski
file - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
file - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
file - Static variable in class org.jmol.script.Token
filecachedirectory - Static variable in class org.jmol.script.Token
filecaching - Static variable in class org.jmol.script.Token
fileName - Variable in class etomica.action.WriteConfiguration
filename - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
filename - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
filename - Variable in class etomica.interfacial.ConfigurationLammps
filename - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
filename - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
filename - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
filename - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
filename - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
filename - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
filename - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
filename - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
filename - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
filename - Variable in class etomica.normalmode.SimBennet.SimBennetParam
filename - Static variable in class etomica.normalmode.SimFluidSoftSphere
filename - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
filename - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
filename - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
filename - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
filename - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
filename - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
filename - Variable in class etomica.normalmode.WriteS
fileName - Variable in class etomica.util.ReadParameters
fileName - Variable in class etomica.util.WriteParameters
filenameB - Variable in class etomica.util.numerical.B9Optimizer.VirialParam
filenameB - Variable in class etomica.util.numerical.VirialOptimizer.VirialParam
filenameP - Variable in class etomica.util.numerical.B9Optimizer.VirialParam
filenameP - Variable in class etomica.util.numerical.VirialOptimizer.VirialParam
fileNameSuffix - Variable in class etomica.data.DataLogger
filePat - Variable in class etomica.potential.P2HydrogenHindePatkowski
filePat - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
files - Variable in class etomica.graph.view.rasterizer.SVGConverter: Contents of fileset elements.
fileWriter - Variable in class etomica.association.MCMoveVolumeAssociated
fileWriter - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
fileWriter - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
fileWriter - Variable in class etomica.data.DataLogger
fileWriter - Variable in class etomica.dimer.IntegratorDimerMin
fileWriter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
fill(int, int, int, int, int, int, int) - Method in class etomica.models.water.P2WaterSzalewicz
fill(int, int) - Method in class etomica.util.RandomNumberGeneratorUnix: Fills the byte buffer with random bytes up to numBytes, starting at offset.
fill - Static variable in class org.jmol.script.Token
fill3j(int, int, int) - Method in class etomica.potential.P2HydrogenPatkowski
fill3j(int, int, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
fill_Vlongdata() - Method in class etomica.potential.P2HydrogenPatkowski
fill_Vlongdata() - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
fillArrays() - Method in class etomica.zeolite.MSDProcessor
fillConeSceen3f(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
fillConeScreen(byte, int, Point3i, Point3i, boolean) - Method in class org.jmol.g3d.Graphics3D
fillCylinder(byte, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
fillCylinderBits(byte, int, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
fillCylinderScreen(byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fillCylinderScreen3I(byte, int, Point3i, Point3i, Point3f, Point3f, float) - Method in class org.jmol.g3d.Graphics3D
fillCylinderXYZ(short, short, byte, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
fillData() - Method in class etomica.potential.P2HydrogenHinde
fillData() - Method in class etomica.potential.P2HydrogenHindeAtomic
fillData() - Method in class etomica.potential.P2NitrogenHellmann
fillData() - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
fillEllipsoid(Point3f, Point3f[], int, int, int, int, Matrix3f, double[], Matrix4f, int, Point3i[]) - Method in class org.jmol.g3d.Graphics3D
fillHermite(int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
fillNeighborListArray(int, int, NeighborListManager, IBox) - Method in class etomica.threaded.atom.PotentialMasterListWorker
fillQuadrilateral(Point3f, Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
fillQuadrilateral3i(Point3i, short, short, Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.g3d.Graphics3D
fillRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D: fills background rectangle for label
fillSphere(int, Point3f) - Method in class org.jmol.g3d.Graphics3D: fills a solid sphere
fillSphereI(int, Point3i) - Method in class org.jmol.g3d.Graphics3D: fills a solid sphere
fillSphereXYZ(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D: fills a solid sphere
fillTriangle(Point3i, short, short, Point3i, short, short, Point3i, short, short, float) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3CN(Point3i, short, short, Point3i, short, short, Point3i, short, short) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3f(Point3f, Point3f, Point3f, boolean) - Method in class org.jmol.g3d.Graphics3D
fillTriangle3i(Point3i, Point3i, Point3i, Point3f, Point3f, Point3f) - Method in class org.jmol.g3d.Graphics3D
fillTriangleTwoSided(short, int, int, int, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
filter - Variable in class etomica.modules.droplet.MeterDeformation
filter - Variable in class etomica.modules.pistoncylinder.ApiFilteredCylinder
filter(Dimension, LinkedList) - Static method in class etomica.units.UnitFilter
filter(Dimension, String[]) - Static method in class etomica.units.UnitFilter
FILTER_HAS_ARTICULATION_PAIR - Static variable in interface etomica.graph.engine.Parser
FILTER_HAS_ARTICULATION_POINT - Static variable in interface etomica.graph.engine.Parser
FILTER_HAS_NO_ROOT_EDGE - Static variable in interface etomica.graph.engine.Parser
FILTER_HAS_NODAL_POINT - Static variable in interface etomica.graph.engine.Parser
FILTER_IS_BICONNECTED - Static variable in interface etomica.graph.engine.Parser
FILTER_IS_CONNECTED - Static variable in interface etomica.graph.engine.Parser
filteredType - Variable in class etomica.atom.iterator.AtomIteratorBasisFilteredType
filteredType - Variable in class etomica.atom.iterator.AtomIteratorLeafFilteredType
filteredType1 - Variable in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
filteredType2 - Variable in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
finalizeOutput() - Method in class org.jmol.g3d.Graphics3D
findAxis(Point3f[], int, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
FindBetaN2AngleFromParameter - Class in etomica.models.nitrogen: Class that creates: 1.
FindBetaN2AngleFromParameter(ISpace, double, double[][]) - Constructor for class etomica.models.nitrogen.FindBetaN2AngleFromParameter
findCandidates() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
findCandidates() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
findcf(double, double, double) - Method in class etomica.normalmode.MinimizeHCP
findDensityAlpha(double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
findDensityatP(double, int, int, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
findDensityBeta(double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
findMaxScore(boolean, ClusterDiagram, int[]) - Static method in class etomica.virial.cluster.ClusterGenerator: Determines whether any cluster permuted from the given one by exchanging points from startPoint to stopPoint (inclusive) has a higher score than that passed in.
findNextCollider() - Method in class etomica.integrator.IntegratorHard: Loops through all atoms to identify the one with the smallest value of collisionTime Collision time is obtained from the value stored in the Integrator.Agent from each atom.
findOppositeAtomIndex(IAtom, IAtomList) - Method in class etomica.normalmode.P1ConstraintNbr: find atom in list that is opposite atomi from atomj (as defined by drj)
findOptParameter(double, double, double[], int) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
findOptParameter(double, double, double[], int) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
findOptParameter(double, double, double[], int) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
findOptParameter(double, double, double[], int) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
findOptRatio(double, double) - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
findPair - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
findPair - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
findPair - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
findPair - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
findPair - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
findPair - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
findPair - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
findPair - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
findPair - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
findPair - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
findPair - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
FindPairMoleculeIndex - Class in etomica.models.nitrogen: Class to identify the pair of molecules that are the same in terms of displacement vector and orientation This is done to speed up the construction of the Hessian Matrix such that we do not have to recalculate the block matrix that is the same.
FindPairMoleculeIndex(ISpace, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.FindPairMoleculeIndex
FindPairMoleculeIndexBetaN2 - Class in etomica.models.nitrogen: BETA-NITROGEN MODEL Class to identify the pair of molecules that are the same in terms of displacement vector and orientation This is done to speed up the construction of the Hessian Matrix such that we do not have to recalculate the block matrix that is the same.
FindPairMoleculeIndexBetaN2(ISpace, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
findParameter() - Method in class etomica.util.numerical.NonLinearCurveDiffFitting
findParameter() - Method in class etomica.util.numerical.NonLinearCurveFitting
findSegmentDepth(List, int) - Static method in class etomica.graph.property.FFTDecomposition
findTetherBonds() - Method in class etomica.modules.sam.Sam
FindTransitionTemperature - Class in etomica.models.nitrogen: Class that determines the transition properties for alpha and beta nitrogen
FindTransitionTemperature(double[], double, double, String) - Constructor for class etomica.models.nitrogen.FindTransitionTemperature
findTransP(int, int, int, double, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
findTransTemperature(double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
finished - Variable in class etomica.potential.PotentialMaster.AtomIterator0
finished - Variable in class etomica.potential.PotentialMaster.MoleculeIterator0
finished - Variable in class etomica.threaded.atom.PotentialMasterListWorker
finished - Variable in class etomica.threaded.domain.PotentialMasterListWorker
finiteDifferenceDerivative - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
FiniteDifferenceDerivative - Class in etomica.util.numerical
FiniteDifferenceDerivative(FunctionMultiDimensional) - Constructor for class etomica.util.numerical.FiniteDifferenceDerivative
FiniteDifferenceDerivativeCG - Class in etomica.conjugategradient
FiniteDifferenceDerivativeCG(IBox, PotentialMaster, AnalyticalDerivativeEnergyParacetamol, ISpace) - Constructor for class etomica.conjugategradient.FiniteDifferenceDerivativeCG
FiniteDifferenceDerivativeCG.MyAgentSource - Class in etomica.conjugategradient
FiniteDifferenceDerivativeCGNitrogenBeta - Class in etomica.models.nitrogen: Finite Difference Derivative Class that is used by Conjugate Gradients related classes This class returns the potential energy and the first derivative of lattice energy PAY ATTENTION to variable: fixedDeltaU
FiniteDifferenceDerivativeCGNitrogenBeta(IBox, PotentialMaster, CoordinateDefinition) - Constructor for class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
FiniteLattice - Interface in etomica.lattice: Interface for a lattice that has a finite, adjustable size.
fireDataChangedEvent() - Method in class etomica.data.DataSet
fireDataCountChangedEvent() - Method in class etomica.data.DataSet
fireEvent(IEvent) - Method in class etomica.action.activity.ControllerEventManager
fireEvent(MouseEvent) - Method in class etomica.graphics.DeviceTernarySelector.MyEventManager
fireEvent(IEvent) - Method in class etomica.graphics.DeviceTernarySelector.MyEventManager
fireEvent(IEvent) - Method in class etomica.integrator.mcmove.MCMoveEventManager
fireEvent(IEvent) - Method in interface etomica.util.IEventManager
fireRowCountChangedEvent() - Method in class etomica.data.DataSinkTable
firingEvent() - Method in interface etomica.api.IIntegratorEventManager: Returns true if the event manager is currently firing events.
firingEvent() - Method in class etomica.integrator.IntegratorEventManager
first - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
first - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
first - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
first - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
first - Variable in class etomica.potential.PotentialGroup
first - Variable in class etomica.util.EventManager
first - Static variable in class org.jmol.script.Token
firstBlock - Variable in class etomica.data.AccumulatorAverageFixed
firstBlock - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
firstBox - Variable in class etomica.integrator.mcmove.MCMoveVolumeExchange
firstDerivative - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
firstElement() - Method in class etomica.util.TreeList: returns the object from the binary tree associated with the lowest sort-key, or null if the tree is empty
firstIsotope - Static variable in class org.jmol.util.Elements: first entry of an actual isotope int the altElementSymbols, altElementNames, altElementNumbers arrays
firstM - Variable in class etomica.lattice.IndexIteratorIncreasing
firstRangeIndependent - Variable in class etomica.nbr.PotentialGroupNbr
firstThread - Variable in class etomica.action.activity.ActivityGroupParallel
firstValue - Variable in class etomica.util.HistogramCollapsing
firstValueCount - Variable in class etomica.util.HistogramCollapsing
fit - Variable in class etomica.surfacetension.SurfaceTensionMapped
fit3b() - Method in class etomica.models.water.P2WaterSzalewicz
fitData - Variable in class etomica.modules.interfacial.FitTanh
fitData - Variable in class etomica.surfacetension.FitTanh
fitDataInfo - Variable in class etomica.modules.interfacial.FitTanh
fitDataInfo - Variable in class etomica.surfacetension.FitTanh
FitTanh - Class in etomica.modules.interfacial
FitTanh() - Constructor for class etomica.modules.interfacial.FitTanh
FitTanh - Class in etomica.surfacetension
FitTanh() - Constructor for class etomica.surfacetension.FitTanh
fitter - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
fitter - Variable in class etomica.util.numerical.AkimaSplineSmootherApp.IntegratorSmoother
fitter - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
fitter - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.IntegratorSmoother
FittingFunctionNonLinear - Class in etomica.util.numerical: This class is coded for specific nonlinear model that decribes the Equation: f(x) = polynomialA + exp(-Kx^L)*polynomialB M and N are the input parameters that determine the order of polynomialA and polynomialB respectively polynomialA is given as: M polynomialA = sum [ a_m * x^m ] m=1 for example, when M=3; polynomialA = a_1 * x + a_2 * x^2 + a_3 * x^3 Note: polynomialB has same form as polynomialA
FittingFunctionNonLinear(int, int) - Constructor for class etomica.util.numerical.FittingFunctionNonLinear
FittingFunctionNonLinearB - Class in etomica.util.numerical: This class is coded for specific nonlinear model that decribes the Equation: f(x) = [ 1 + exp(-Kx^L) ] * polynomialA M is the input parameter that determine the order of polynomialA polynomialA is given as: M polynomialA = sum [ a_m * x^m ] m=1 for example, when M=3; polynomialA = a_1 * x + a_2 * x^2 + a_3 * x^3
FittingFunctionNonLinearB(int) - Constructor for class etomica.util.numerical.FittingFunctionNonLinearB
fivea - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
fixed - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
fixed - Variable in class etomica.dimer.SimDimerLJadatom
fixed - Variable in class etomica.dimer.SimDimerLJgb
fixed - Variable in class etomica.dimer.SimDimerMEAMadatom
fixed - Variable in class etomica.dimer.SimDimerMEAMGB
fixed - Variable in class etomica.kmc.SimKMCLJadatom
fixed - Variable in class etomica.kmc.SimKMCMEAMadatom
fixedCOM - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
fixedDaDef - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
fixedDaDef - Variable in class etomica.normalmode.SimLJVacancy.LJParams
FixedEdgeCountIterator - Class in etomica.graph.iterators
FixedEdgeCountIterator(byte, byte) - Constructor for class etomica.graph.iterators.FixedEdgeCountIterator
fixedLatticeVector - Variable in class etomica.models.hexane.PrimitiveHexane
fixedRvdw - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
fixedRvdw - Variable in class etomica.potential.P2QChemInterpolated
fixedRvdw - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
fixedRvdw - Variable in class etomica.potential.P3QChem.DampingParams
fixedSizes - Variable in class etomica.models.hexane.PrimitiveHexane
fixedSpecies - Variable in class etomica.config.GrainBoundaryTiltConfiguration
FixedSumIterator - Class in etomica.math.discrete: Generates int[] arrays such that the sum of (k+1) * array[k] over the elements of array are equal to a given value.
FixedSumIterator(int) - Constructor for class etomica.math.discrete.FixedSumIterator
FixedWall - Class in etomica.interfacial
FixedWall(ISpace, IBox, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>, ISpecies) - Constructor for class etomica.interfacial.FixedWall
fixedWall - Variable in class etomica.interfacial.IntegratorFixedWall
fixedWall - Variable in class etomica.interfacial.LJMD.LJMDParams
fixOverlap - Variable in class etomica.association.MCMoveDimer
fixOverlap - Variable in class etomica.association.MCMoveDimerRotate
fixOverlap - Variable in class etomica.association.MCMoveSmer
fixOverlap - Variable in class etomica.association.MCMoveSmerRotate
fixOverlap - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
fixOverlap - Variable in class etomica.integrator.mcmove.MCMoveAtom
fixOverlap - Variable in class etomica.integrator.mcmove.MCMoveDimer
fixOverlap - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
fixOverlap - Variable in class etomica.models.hexane.MCMoveReptate
fixPistonButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
fk - Variable in class etomica.virial.CalcFFT
fL - Variable in class etomica.virial.ClusterSinglyConnected
flag - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
FLAG - Static variable in class etomica.potential.P2HardAssociationCone
FLAG - Static variable in class etomica.potential.P2HardAssociationConeDoubleSites
FLAG - Static variable in class etomica.potential.P2HardAssociationConeFourSites
FLAG - Static variable in class etomica.potential.P2HardAssociationConeFourSitesSW
FLAG - Static variable in class etomica.potential.P2HardAssociationConeOneSite
FLAG - Static variable in class etomica.potential.P2HardAssociationConeReference
FLAG - Static variable in class etomica.potential.P2HardAssociationConeReferenceFourSites
FLAG - Static variable in class etomica.potential.P2HardAssociationConeSW
flag - Static variable in class etomica.potential.P2WaterPotentialsJankowski
flag1 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
flex - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
flex - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
flex - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
flex - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
flex - Variable in class etomica.virial.cluster.VirialDiagrams
flex - Variable in class etomica.virial.cluster.VirialDiagramsMix
flex - Variable in class etomica.virial.cluster.VirialDiagramsMix2
flex - Variable in class etomica.virial.cluster.VirialDiagramsPT
flex - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
flex - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
flex - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
flexApproach - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
flexCancelOnly - Variable in class etomica.virial.cluster.VirialDiagrams
flexCancelOnly - Variable in class etomica.virial.cluster.VirialDiagramsPT
flexColors - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
flexColors - Variable in class etomica.virial.cluster.VirialDiagrams
flexColors - Variable in class etomica.virial.cluster.VirialDiagramsMix
flexColors - Variable in class etomica.virial.cluster.VirialDiagramsMix2
flexColors - Variable in class etomica.virial.cluster.VirialDiagramsPT
flexID - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
flexID - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
flexID - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
flexID - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
flexID - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
flexID - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
flexOnlyTerm - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
flip - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
flip - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
flip - Static variable in class etomica.potential.P2WaterPotentialsJankowski
flip(IMolecule) - Method in class etomica.virial.ClusterCoupledAtomFlipped
flip(IMolecule) - Method in class etomica.virial.ClusterCoupledFlipped
flipBit(int) - Method in interface etomica.graph.model.Bitmap
flipBit(int) - Method in class etomica.graph.model.impl.AbstractBitmap
flipList - Variable in class etomica.virial.ClusterCoupledFlippedPartial
flippedAtoms - Variable in class etomica.virial.ClusterCoupledFlipped
flippedAtoms - Variable in class etomica.virial.ClusterCoupledFlippedPartial
flistValue(Token, int) - Static method in class org.jmol.script.ScriptVariable
fLN - Variable in class etomica.virial.ClusterSinglyConnected
FloatOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.FloatOptionHandler
floatparam - Static variable in class org.jmol.script.Token
floatproperty - Static variable in class org.jmol.script.Token
floatValue() - Method in class etomica.veos.bigdecimal.BigSurd: Return a float value representation.
floatValue() - Method in class etomica.veos.bigdecimal.BigSurdVec: Construct an approximate floating point representation
floatValue() - Method in class etomica.veos.bigdecimal.Rational: Return a float value representation.
floodCircle(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
floodInside(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
floor() - Method in class etomica.veos.bigdecimal.Rational: floor(): the nearest integer not greater than this.
flowLines - Variable in class etomica.modules.rheology.RheologyGraphic
fluctuationFactor - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
fluctuationFromAvg - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
fluid - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
Fluoride - Class in etomica.chem.elements: Class for the Fluoride element.
Fluoride(String) - Constructor for class etomica.chem.elements.Fluoride
Fluoride(String, double) - Constructor for class etomica.chem.elements.Fluoride
flushImage(Object) - Method in interface org.jmol.api.ApiPlatform
flushImage(Object) - Method in class org.jmol.awt.Platform
flushShades() - Static method in class org.jmol.util.Colix
flushSphereCache() - Static method in class org.jmol.util.Shader
fluxAccumulator - Variable in class etomica.modules.dcvgcmd.DCVGCMD
fluxMeters - Variable in class etomica.modules.dcvgcmd.DCVGCMD
fMap - Variable in class etomica.virial.ClusterWheatleySoftBDMix
fMap - Variable in class etomica.virial.ClusterWheatleySoftMix
fMap3 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
fmBond - Variable in class etomica.virial.cluster.VirialDiagrams
fmBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
Fmin - Variable in class etomica.dimer.IntegratorDimerMin
Fmin2 - Variable in class etomica.dimer.IntegratorDimerMin
Fmin2perp - Variable in class etomica.dimer.IntegratorDimerMin
Fmin2star - Variable in class etomica.dimer.IntegratorDimerMin
Fminperp - Variable in class etomica.dimer.IntegratorDimerMin
Fminstar - Variable in class etomica.dimer.IntegratorDimerMin
fMulti - Variable in class etomica.virial.ClusterWheatleyMultibody
fMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
fname - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
fname - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
fname - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
fname - Variable in class etomica.normalmode.SimOverlapSoftSphere
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
fname - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
fname - Variable in class etomica.normalmode.SimOverlapSSnxy
fNonAdditive - Variable in class etomica.virial.ClusterSumMultibody
fNonAdditive - Variable in class etomica.virial.ClusterWheatleyMultibody
fNonAdditive - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
fNonAdditiveNeeded - Variable in class etomica.virial.ClusterSumMultibody
fNonAdditiveValues - Variable in class etomica.virial.ClusterSumMultibody
focusGained(FocusEvent) - Method in class etomica.graphics.PropertyText
focusLost(FocusEvent) - Method in class etomica.graphics.PropertyText
fOld - Variable in class etomica.virial.ClusterSum
fOld - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
fOld - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
fOld - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
fOld - Variable in class etomica.virial.ClusterTree
font - Variable in class org.jmol.util.JmolFont
FONT_FACE_MONO - Static variable in class org.jmol.util.JmolFont
FONT_FACE_SANS - Static variable in class org.jmol.util.JmolFont
FONT_FACE_SERIF - Static variable in class org.jmol.util.JmolFont
FONT_STYLE_BOLD - Static variable in class org.jmol.util.JmolFont
FONT_STYLE_BOLDITALIC - Static variable in class org.jmol.util.JmolFont
FONT_STYLE_ITALIC - Static variable in class org.jmol.util.JmolFont
FONT_STYLE_PLAIN - Static variable in class org.jmol.util.JmolFont
fontcaching - Static variable in class org.jmol.script.Token
fontFace - Variable in class org.jmol.util.JmolFont
fontscaling - Static variable in class org.jmol.script.Token
fontSize - Variable in class org.jmol.util.JmolFont
fontSizeNominal - Variable in class org.jmol.util.JmolFont
fontStringWidth(JmolFont, Object, String) - Method in interface org.jmol.api.ApiPlatform
fontStringWidth(JmolFont, Object, String) - Method in class org.jmol.awt.Platform
fontStyle - Variable in class org.jmol.util.JmolFont
foo() - Method in class etomica.modules.clustergenerator.MyApplet.Starter
foo() - Method in class etomica.modules.droplet.IntegratorDroplet
foo - Static variable in class etomica.virial.MCMoveClusterDiagram
foo2 - Static variable in class etomica.virial.MCMoveClusterDiagram
footerPanel - Variable in class etomica.graphics.SimulationPanel
force() - Method in interface etomica.integrator.Integrator.Forcible
force - Variable in class etomica.integrator.IntegratorConNVT.Agent
force() - Method in class etomica.integrator.IntegratorConNVT.Agent
force - Variable in class etomica.integrator.IntegratorGear4.Agent
force() - Method in class etomica.integrator.IntegratorGear4.Agent
force - Variable in class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
force() - Method in class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
force - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.AtomAgent
force() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.AtomAgent
force - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
force() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
force - Variable in class etomica.integrator.IntegratorVelocityVerlet.MyAgent
force() - Method in class etomica.integrator.IntegratorVelocityVerlet.MyAgent
force - Variable in class etomica.integrator.IntegratorVerlet.Agent
force() - Method in class etomica.integrator.IntegratorVerlet.Agent
force - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
force() - Method in class etomica.modules.droplet.IntegratorDroplet.MyAgent
force - Variable in class etomica.modules.materialfracture.P1Tension
force() - Method in class etomica.normalmode.LJVacancyMin.VectorForce
force(IAtomList) - Method in class etomica.potential.P2TriangleWell
force - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.AtomAgent
force() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion.AtomAgent
force - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
Force - Class in etomica.units: Base for all force units.
force() - Method in class etomica.units.systems.CGS
force() - Method in class etomica.units.systems.LJ
force() - Method in class etomica.units.systems.MKS
force() - Method in class etomica.units.systems.UnitSystem
force() - Method in class etomica.units.systems.UnitSystem.Sim
force0 - Variable in class etomica.dimer.IntegratorDimerMin
force0 - Variable in class etomica.dimer.IntegratorDimerRT
force1 - Variable in class etomica.dimer.IntegratorDimerRT
force2 - Variable in class etomica.dimer.IntegratorDimerRT
forceAgentManager - Variable in class etomica.surfacetension.SurfaceTensionMapped
forceautobond - Static variable in class org.jmol.script.Token
forceComputed() - Method in class etomica.integrator.IntegratorEventManager
forceConstant - Variable in class etomica.util.numerical.CalcGradientDifferentiable
forced - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
forced - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
forcefield - Static variable in class org.jmol.script.Token
forceGauss - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
forceManager - Variable in class etomica.mappedvirial.MappedUpotential
forceManager - Variable in class etomica.mappedvirial.MeterMappedU
forceManager - Variable in class etomica.mappedvirial.MeterMappedVirial
forceManager - Variable in class etomica.mappedvirial.MeterMappedVirialV
forceManager - Variable in class etomica.mappedvirial.MeterMeanForce
forceManager - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
forceManager - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
forceManager - Variable in class etomica.normalmode.MeterDADB
forceManager - Variable in class etomica.normalmode.MeterSolidProps
forceManager - Variable in class etomica.normalmode.MeterSolidPropsLJ
forceMin - Variable in class etomica.dimer.IntegratorDimerMin
forceSum - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
forceSum - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
forceSum - Variable in class etomica.integrator.IntegratorConNVT
forceSum - Variable in class etomica.integrator.IntegratorVelocityVerlet
forceSum - Variable in class etomica.integrator.IntegratorVelocityVerletShake
forceSum - Variable in class etomica.integrator.IntegratorVerlet
forceSum - Variable in class etomica.modules.droplet.IntegratorDroplet
forceSum - Variable in class etomica.modules.rosmosis.ReverseOsmosis
forceSum - Variable in class etomica.modules.sam.Sam
forceSum - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
forceSumNPH - Variable in class etomica.integrator.IntegratorGear4NPH
ForceSumNPH(ISpace) - Constructor for class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
FORMAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
FORMAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
FORMAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
FORMAL_CHARGE_INDEX_MAX - Static variable in class org.jmol.viewer.JmolConstants
FORMAL_CHARGE_INDEX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
FORMAL_CHARGE_MAX - Static variable in class org.jmol.util.Elements
FORMAL_CHARGE_MIN - Static variable in class org.jmol.util.Elements: ionic radii are looked up using an array of shorts (16 bits each) that contains the atomic number, the charge, and the radius in two consecutive values, encoded as follows: (atomicNumber << 4) + (charge + 4), radiusAngstroms*1000 That is, (atomicNumber * 16 + charge + 4), milliAngstromRadius This allows for charges from -4 to 11, but we only really have -4 to 7.
FORMAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
formalcharge - Static variable in class org.jmol.script.Token
format(double, int) - Static method in class etomica.graphics.DisplayTextBox: Formats a double with a specified number of digits.
format(double, StringBuffer, FieldPosition) - Method in class etomica.util.ScientificFormat
format(long, StringBuffer, FieldPosition) - Method in class etomica.util.ScientificFormat
format - Static variable in class org.jmol.script.Token
formatCheck(String) - Static method in class org.jmol.util.TextFormat: formatCheck checks p and q formats and duplicates if necessary "%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
formatD(double, int, int, boolean, boolean, boolean) - Static method in class org.jmol.util.TextFormat
formatDecimal(float, int) - Static method in class org.jmol.util.TextFormat: a simple alternative to DecimalFormat (which Java2Script does not have and which is quite too complex for our use here.
formatF(float, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
formatMessage(String, Object[]) - Static method in class etomica.graph.view.rasterizer.Messages: Implements Localizable.formatMessage(String,Object[]).
formatS(String, int, int, boolean, boolean) - Static method in class org.jmol.util.TextFormat
formatStringF(String, String, float) - Static method in class org.jmol.util.TextFormat
formatStringI(String, String, int) - Static method in class org.jmol.util.TextFormat
formatStringS(String, String, String) - Static method in class org.jmol.util.TextFormat
formatter - Variable in class etomica.graphics.DisplayTable
forward(double[], double) - Static method in class etomica.util.SineTransform
forwardDataMap - Variable in class etomica.data.DataSet
foundRing - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
foura - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
FourAssociationSitesFluid2Pt - Class in etomica.virial.simulations: Wertheim 2 point diagram simulation using Mayer sampling for four association sites model
FourAssociationSitesFluid2Pt() - Constructor for class etomica.virial.simulations.FourAssociationSitesFluid2Pt
FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
Fourier() - Constructor for class etomica.util.Transform.Fourier
fourierMul(Graph, Graph, byte) - Static method in class etomica.virial.IEGenerator
foursqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
foursqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
Fpara - Variable in class etomica.dimer.IntegratorDimerMin
Fpara - Variable in class etomica.dimer.IntegratorDimerRT
fparams - Static variable in class etomica.models.co2.P2CO2H2OWheatley
Fperp - Variable in class etomica.dimer.IntegratorDimerMin
Fperp - Variable in class etomica.dimer.IntegratorDimerRT
Fperplast - Variable in class etomica.dimer.IntegratorDimerRT
fPrime - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
fPrime - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
Fprimerot - Variable in class etomica.dimer.IntegratorDimerMin
Fprimerot - Variable in class etomica.dimer.IntegratorDimerRT
fPrimeRotation - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
fQ - Variable in class etomica.modules.rheology.IntegratorPolymer
fQ - Variable in class etomica.virial.ClusterSumHS
fQ - Variable in class etomica.virial.ClusterWheatleyExtendSW
fQ - Variable in class etomica.virial.ClusterWheatleyHS
fQ - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fQ - Variable in class etomica.virial.ClusterWheatleySoft
fQ - Variable in class etomica.virial.ClusterWheatleySoftBD
fQmulti - Variable in class etomica.virial.ClusterWheatleyMultibody
fQmulti - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
fQQ - Variable in class etomica.virial.ClusterWheatleyExtendSW
Fr - Variable in class etomica.dimer.IntegratorDimerRT
fr - Variable in class etomica.virial.CalcFFT
FR2() - Constructor for class etomica.virial.ClusterSumIC.FR2
frac - Variable in class etomica.normalmode.MCMoveHarmonicEin
frac - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
frac - Variable in class etomica.normalmode.MeterBoltzmannTarget
frac - Variable in class etomica.normalmode.MeterOverlapSwitch
frac - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
frac - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
frac - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
frac - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
fracSource - Variable in class etomica.overlap.IntegratorOverlap
Fraction - Class in etomica.units: Dimension for a quantity representing a fractional amount.
fraction() - Method in class etomica.units.systems.CGS
fraction() - Method in class etomica.units.systems.LJ
fraction() - Method in class etomica.units.systems.MKS
fraction() - Method in class etomica.units.systems.UnitSystem
fraction() - Method in class etomica.units.systems.UnitSystem.Sim
fractionalrelative - Static variable in class org.jmol.script.Token
fractionTabulated() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
fracx - Static variable in class org.jmol.script.Token
fracxyz - Static variable in class org.jmol.script.Token
fracy - Static variable in class org.jmol.script.Token
fracz - Static variable in class org.jmol.script.Token
frank - Static variable in class org.jmol.script.Token
fRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
fRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
fRBond - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
fRBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
fRBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
fReader - Variable in class etomica.util.RandomNumberGeneratorUnix
FreeRadicalPolymerizationGraphic - Class in etomica.modules.chainequilibrium: Module for chain reaction (polymerization) using ChainEquilibriumSim as the simulation class.
FreeRadicalPolymerizationGraphic(FreeRadicalPolymerizationSim, ISpace) - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
FreeRadicalPolymerizationGraphic.Applet - Class in etomica.modules.chainequilibrium
FreeRadicalPolymerizationSim - Class in etomica.modules.chainequilibrium
FreeRadicalPolymerizationSim() - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
FreeRadicalPolymerizationSim(ISpace) - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
fRef - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
fRefPos - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
fRefPos - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
frequencies - Variable in class etomica.dimer.SimDimerLJadatom
frequencies - Variable in class etomica.dimer.SimDimerMEAMadatom
frequencies - Variable in class etomica.dimer.SimDimerMEAMGB
frequencies - Variable in class etomica.kmc.SimKMCMEAMadatom
fromSim(double) - Method in class etomica.units.CompoundUnit
fromSim(double) - Method in class etomica.units.PrefixedUnit: Takes the given value in simulation units and converts it to class units (considering prefix).
fromSim(double) - Method in class etomica.units.SimpleUnit: Takes the given value in simulation units and converts it to class units.
fromSim(double) - Method in class etomica.units.systems.LJ.LJUnit
fromSim(double) - Method in interface etomica.units.Unit: Takes the given value in simulation units and converts it to class units (considering prefix).
FRONT - Static variable in class etomica.util.Constants.Direction
front - Static variable in class org.jmol.script.Token
frontlit - Static variable in class org.jmol.script.Token
frontonly - Static variable in class org.jmol.script.Token
Frot - Variable in class etomica.dimer.IntegratorDimerMin
Frot - Variable in class etomica.dimer.IntegratorDimerRT
Frot2 - Variable in class etomica.dimer.IntegratorDimerRT
fShift - Variable in class etomica.potential.P2SoftSphericalTruncatedForceShifted
fShift - Variable in class etomica.rotation.P2LJDipole
Fstar - Variable in class etomica.dimer.IntegratorDimerMin
Fstar - Variable in class etomica.dimer.IntegratorDimerRT
Fstarperp - Variable in class etomica.dimer.IntegratorDimerMin
Fstarperp - Variable in class etomica.dimer.IntegratorDimerRT
fTargete2 - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
fTargetf1 - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
fType - Variable in class etomica.virial.Species7SiteRigidSF6
fudge - Variable in class etomica.models.hexane.SimHarmonicHexane
full(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: This function will tell the user, if passed an atom weither or not that atom can bond
Full - Class in etomica.virial.cluster
Full(int) - Constructor for class etomica.virial.cluster.Full: Constructor for a fully joined cluster
full(int) - Static method in class etomica.virial.cluster.Standard: Returns a full set of bonds, such that each of the n points is joined to each of the others.
full(int, int) - Static method in class etomica.virial.cluster.Standard: Returns a full set of bonds, such that each of the n points is joined to each of the others; starts labeling of point using the given index .
full - Static variable in class org.jmol.script.Token
fullBondColorMap - Variable in class etomica.modules.catalysis.ColorSchemeRadical
fullBondIndexArray - Variable in class etomica.virial.ClusterSum
fullBondMask - Variable in class etomica.virial.ClusterSumHS
fullBondMask - Variable in class etomica.virial.ClusterWheatleyHS
fullBondMask - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
fullColorMap - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
fullCovariance - Variable in class etomica.data.AccumulatorAverageCovariance
fullLnN - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
fullLnXi - Variable in class etomica.virial.cluster.VirialDiagrams
fullLnXi - Variable in class etomica.virial.cluster.VirialDiagramsPT
fullMultiP - Variable in class etomica.virial.cluster.VirialDiagrams
fullMultiP - Variable in class etomica.virial.cluster.VirialDiagramsPT
fullOverlapResult - Variable in class etomica.virial.overlap.DataVirialOverlap
fullRatioResult - Variable in class etomica.virial.overlap.DataVirialOverlap
FullResult() - Constructor for class etomica.virial.overlap.DataVirialOverlap.FullResult
fullSystemResult - Variable in class etomica.virial.overlap.DataVirialOverlap
fullylit - Static variable in class org.jmol.script.Token
funcs - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
funcs - Variable in class etomica.util.numerical.NonLinearCurveFitting
function(IVector, IVector, IVector, double, double) - Method in class etomica.normalmode.PotentialCalculationEFSSP
function(IVector, IVector, IVector, double, double) - Method in class etomica.normalmode.PotentialCalculationLJSP
Function - Interface in etomica.util: Interface for the basic features of a function that maps a double onto another double.
function - Variable in class etomica.util.FunctionChain.Link
function - Variable in class etomica.util.numerical.Function1d
Function.Abs - Class in etomica.util: The function f(x) = abs(x)
Function.Chop - Class in etomica.util: Returns the input value if its magnitude is greater than value specified at construction; otherwise returns zero.
Function.Constant - Class in etomica.util: The function f(x) = constant
Function.Exp - Class in etomica.util: The function f(x) = exp(x)
Function.Identity - Class in etomica.util: The function f(x) = x
Function.Linear - Class in etomica.util: The function f(x) = a*x + b
Function.Log - Class in etomica.util: The function f(x) = ln(x)
Function.Reciprocal - Class in etomica.util: The function f(x) = 1/x
Function.Sqrt - Class in etomica.util: The function f(x) = sqrt(x)
Function1d - Class in etomica.util.numerical
Function1d() - Constructor for class etomica.util.numerical.Function1d
Functional - Interface in etomica.util: Interface for the basic features of a functional, which maps a function onto a double.
FunctionB2LJQ() - Constructor for class etomica.modules.vle.B2Fit.FunctionB2LJQ
FunctionChain - Class in etomica.util: Defines a function as chain of other functions.
FunctionChain() - Constructor for class etomica.util.FunctionChain
FunctionChain.Link - Class in etomica.util: Class for making linked list of Functions
FunctionDifferentiable - Interface in etomica.util
FunctionGeneral - Interface in etomica.util: Interface for the basic features of a general function that maps an object into Data.
FunctionInvertible - Interface in etomica.util
FunctionMayerB2LJQ() - Constructor for class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
FunctionMultiDimensional - Interface in etomica.util: Interface for multi-dimensional function.
FunctionMultiDimensionalDifferentiable - Interface in etomica.util: Interface for multi-dimensional 1-D differentiable function
functions - Variable in class etomica.virial.MayerFunctionProductGeneral
functions - Variable in class etomica.virial.MayerFunctionSum
functions - Variable in class etomica.virial.MayerFunctionSumGeneral
functionsFile - Variable in class etomica.mappedvirial.MappedU.LJMDParams
functionsFile - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
functionsFile - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
furthestNeighborDelta - Variable in class etomica.lattice.RectangularLatticeNbrIteratorSquare
fux - Static variable in class org.jmol.script.Token
fuxyz - Static variable in class org.jmol.script.Token
fuy - Static variable in class org.jmol.script.Token
fuz - Static variable in class org.jmol.script.Token
fval - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
fValue(Token) - Static method in class org.jmol.script.ScriptVariable
fValues - Variable in class etomica.virial.ClusterChainHS
fValues - Variable in class etomica.virial.ClusterChainSoft
fValues - Variable in class etomica.virial.ClusterSum
fValues - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
fValues - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
fValues - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
fValues - Variable in class etomica.virial.ClusterTree
fw - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
fw - Variable in class etomica.normalmode.MeterDDP
fw - Variable in class etomica.normalmode.MeterDP
fw - Variable in class etomica.normalmode.MeterTargetTP
fWork - Variable in class etomica.models.water.P2Water3PSoft
fWork - Variable in class etomica.models.water.P2Water4PSoft

G

G - Variable in class etomica.math.Gamma
g - Variable in class etomica.modules.droplet.P1Smash
G - Static variable in class etomica.util.Constants: The gravitational constant, in simulation units.
g - Variable in class etomica.virial.ClusterWheatleyExtendSW
g1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
G1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
g1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
G1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
g1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
G2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
g2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
G2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
g2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
G2pBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
G3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
g3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
G3DSys - Class in g3dsys.control: Abstraction and delegation container class to facilitate communication between the CoordMapper, FigureManager, and G3DPanel without deeply coupling them in their own definitions.
G3DSys(Container) - Constructor for class g3dsys.control.G3DSys
g3dsys.control - package g3dsys.control
g3dsys.images - package g3dsys.images
G3pBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
G4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
g4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
G_EARTH - Static variable in class etomica.util.Constants: The standard acceleration of gravity on Earth.
ga - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
ga - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
gamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
gamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
Gamma - Class in etomica.math: This class calculates the incomplete gamma function and complementary incomplete gamma function.
Gamma() - Constructor for class etomica.math.Gamma
gamma(double) - Static method in class etomica.math.SpecialFunctions
gamma() - Method in class etomica.meam.PotentialMEAM
gamma - Variable in class etomica.models.co2.PNCO2GCPM
gamma - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
gamma - Static variable in class etomica.models.water.P2WaterSzalewicz
gamma - Variable in class etomica.models.water.PNWaterGCPM
gamma - Variable in class etomica.normalmode.MeterSolidPropsLJ
gamma(MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Euler-Mascheroni constant.
Gamma(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The Gamma function.
Gamma(Rational, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The Gamma function.
gamma_New - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
gamma_New - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
gamma_Old - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
gamma_Old - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
gammai - Variable in class etomica.dimer.IntegratorDimerRT
gammaQ(double, double) - Static method in class etomica.math.SpecialFunctions: Normalized incomplete gamma function, equal to Integrate[Exp[-t] t^(a-1),{t,x,Infinity}]/Gamma[a]
gaussj(double[][], int, double[][], int) - Static method in class etomica.math.linearalgebra.GaussJordanElimination: Performs Gauss-Jordan elimination in place to solve Ax=b.
GaussJordanElimination - Class in etomica.math.linearalgebra
gb - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
gb - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
gbConst - Variable in class etomica.modules.clustergenerator.MyApplet
gbLayout - Variable in class etomica.modules.clustergenerator.MyApplet
GBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
GBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
GBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
gcd(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Greatest common divisor of this and oth.
gComp - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
gComp - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
GCPMAgent(double, double, double, double, double, double, double, double) - Constructor for class etomica.models.co2.PNGCPM.GCPMAgent
GCPMAgent(double, double, double, double, double, double, double, double, double) - Constructor for class etomica.models.co2.PNGCPM.GCPMAgent
GData - Class in org.jmol.util
GData() - Constructor for class org.jmol.util.GData
geAtomPositionDefinition() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
GEMCWithRotation - Class in etomica.simulation.prototypes: Simple Gibbs-ensemble Monte Carlo simulation of rotating molecules.
GEMCWithRotation(Space) - Constructor for class etomica.simulation.prototypes.GEMCWithRotation
generalizedCoord - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
generalizedCoord - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
generateConfigs(String, double) - Method in class etomica.dimer.SimDimerLJadatom
generateConfigs(String, double) - Method in class etomica.dimer.SimDimerMEAMadatom
generateConfigs(String, double) - Method in class etomica.dimer.SimDimerMEAMGB
generateGraphicsCB - Variable in class etomica.modules.clustergenerator.MyApplet
generateNewU(double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
generator - Variable in class etomica.modules.clustergenerator.MyApplet
Geodesic - Class in org.jmol.util: Consolidated Geodesic from dotsRenderer 3/19/07 Bob Hanson Constructs a canonical geodesic sphere of unit radius.
Geodesic() - Constructor for class org.jmol.util.Geodesic
geosurface - Static variable in class org.jmol.script.Token
gestureswipefactor - Static variable in class org.jmol.script.Token
get(String) - Method in class etomica.compatibility.FeatureSet
get(String) - Static method in class etomica.graph.view.rasterizer.Messages
get(String, String) - Static method in class etomica.graph.view.rasterizer.Messages
get(int) - Method in class etomica.util.ObjectArrayList: Returns the element at the specified position in this list.
get(int) - Method in class org.jmol.util.BitSet: Returns the value of the bit with the specified index.
get(int) - Method in class org.jmol.util.Int2IntHash
get(Vector3f) - Method in class org.jmol.util.Matrix4f: Retrieves the translational components of this matrix.
get2ndDerivative() - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
get2ndDerivative() - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
get2ndDerivative() - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
get2ndDerivativeFile(double[][], String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
get2ndDerivativeMoleculei(CoordinateDefinition, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
get2ndDerivativeMoleculei(CoordinateDefinition, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
get2SidedNormix(Vector3f, BitSet) - Static method in class org.jmol.util.Normix
get3dProjection(Vector3f) - Method in class org.jmol.util.Quaternion
getA() - Method in class etomica.association.MCMoveAtomDimer
getA() - Method in class etomica.association.MCMoveAtomMonomer
getA() - Method in class etomica.association.MCMoveAtomNoSmer
getA() - Method in class etomica.association.MCMoveAtomSmer
getA() - Method in class etomica.association.MCMoveBiasUB
getA() - Method in class etomica.association.MCMoveBiasUBMolecule
getA() - Method in class etomica.association.MCMoveDimer: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.association.MCMoveDimerRotate: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.association.MCMoveMoleculeMonomer
getA() - Method in class etomica.association.MCMoveMoleculeRotateAssociated
getA() - Method in class etomica.association.MCMoveMoleculeSmer
getA() - Method in class etomica.association.MCMoveRotateAssociated
getA() - Method in class etomica.association.MCMoveRotateNoSmer
getA() - Method in class etomica.association.MCMoveSmer: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.association.MCMoveSmerRotate: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.association.MCMoveVolumeAssociated
getA() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
getA() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
getA() - Method in class etomica.integrator.mcmove.MCMove: Returns the temperature-independent part of the acceptance probability.
getA() - Method in class etomica.integrator.mcmove.MCMoveAtom: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
getA() - Method in class etomica.integrator.mcmove.MCMoveDimer: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
getA() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
getA() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
getA() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
getA() - Method in class etomica.integrator.mcmove.MCMoveMolecule: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
getA() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
getA() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
getA() - Method in class etomica.integrator.mcmove.MCMoveVolume
getA() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
getA() - Method in class etomica.math.geometry.Plane
getA() - Method in class etomica.models.hexane.MCMoveCBMC
getA() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
getA() - Method in class etomica.models.hexane.MCMoveReptate
getA() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
getA() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
getA() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
getA() - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
getA() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
getA() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
getA() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
getA() - Method in class etomica.modules.adsorption.MyMCMove
getA() - Method in class etomica.modules.dcvgcmd.MyMCMove
getA() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
getA() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
getA() - Method in class etomica.modules.pistoncylinder.PistonPlane
getA() - Method in class etomica.modules.rheology.IntegratorPolymer
getA() - Method in class etomica.modules.sam.WallPlane
getA() - Method in class etomica.normalmode.MCMoveAtomCoupled
getA() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.normalmode.MCMoveAtomSuperBox: Returns log of the ratio of the trial probabilities, ln(Tij/Tji) for the states encountered before (i) and after (j) the most recent call to doTrial().
getA() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
getA() - Method in class etomica.normalmode.MCMoveHarmonic
getA() - Method in class etomica.normalmode.MCMoveHarmonicStep
getA() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
getA() - Method in class etomica.normalmode.MCMovePhaseAngle
getA() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
getA() - Method in class etomica.normalmode.MCMoveSingleMode
getA() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
getA() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
getA() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
getA() - Method in class etomica.normalmode.MCMoveVolumeSolid
getA() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
getA() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
getA() - Method in class etomica.normalmode.MCMoveWV
getA() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
getA() - Method in class etomica.potential.P2Exp6
getA(int) - Method in class etomica.potential.P2HeSimplified: Returns the ith parameter value u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X where X = 10 if useC10 is true, X=8 otherwise
getA() - Method in class etomica.potential.P2ModifiedMorse
getA() - Method in class etomica.potential.P2Morse
getA() - Method in class etomica.spin.MCMoveSpinFlip
getA() - Method in class etomica.util.numerical.PadeApproximation
getA() - Method in class etomica.virial.MCMoveChangeBondLength
getA() - Method in class etomica.virial.MCMoveClusterAngleBend
getA() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
getA() - Method in class etomica.virial.MCMoveClusterAtom
getA() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
getA() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
getA() - Method in class etomica.virial.MCMoveClusterAtomHSChain
getA() - Method in class etomica.virial.MCMoveClusterAtomHSRing
getA() - Method in class etomica.virial.MCMoveClusterAtomHSTree
getA() - Method in class etomica.virial.MCMoveClusterAtomMulti
getA() - Method in class etomica.virial.MCMoveClusterAtomQ
getA() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
getA() - Method in class etomica.virial.MCMoveClusterDiagram
getA() - Method in class etomica.virial.MCMoveClusterMolecule
getA() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
getA() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
getA() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
getA() - Method in class etomica.virial.MCMoveClusterReptateMulti
getA() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
getA() - Method in class etomica.virial.MCMoveClusterRingRegrow
getA() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
getA() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
getA() - Method in class etomica.virial.MCMoveClusterRingScale
getA() - Method in class etomica.virial.MCMoveClusterRotateCH3
getA() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
getA() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
getA() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
getA() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
getA() - Method in class etomica.virial.MCMoveClusterTorsionMulti
getA() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
getA() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
getA() - Method in class etomica.virial.MCMoveClusterWiggleMulti
getA() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
getAcceptanceTarget() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
getAccumulator() - Method in class etomica.graphics.DisplayTextBoxesCAE: Accessor method for the data source that generates the displayed value.
getAccumulators() - Method in class etomica.data.DataTableAverages: Returns a clone of the accumulator array.
getAccumulators() - Method in class etomica.virial.MeterVirialBDBin
getAccumulators() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
getAccumulators() - Method in class etomica.virial.overlap.DataVirialOverlap
getAccumulatorUpdateInterval() - Method in class etomica.data.DataTableAverages
getAcQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
getAcQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
getAction() - Method in class etomica.action.activity.ControllerEvent
getAction() - Method in class etomica.graphics.DeviceButton: Returns the currently defined action associated with the button.
getAction() - Method in class etomica.integrator.IntegratorAnalytic
getAction() - Method in class etomica.listener.IntegratorListenerAction
getAction() - Method in class etomica.zeolite.DeviceButtonSingle: Returns the currently defined action associated with the button.
getActionStatus(IAction) - Method in class etomica.action.activity.Controller: Returns the status of an action held by the controller.
getActionStatus(IAction) - Method in interface etomica.action.activity.IController: Returns the status of an action held by the controller.
getActivityIntegrate() - Method in class etomica.normalmode.SimOverlapModule
getActualStepFreq0() - Method in class etomica.virial.overlap.IntegratorOverlap
getAddAnotherSpecies() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAddPotential() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAddPotential() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getAddSameSpecies() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAddSpecies() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAddSpecies1() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAddSpecies2() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAddSpecies3() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getADimension() - Method in class etomica.potential.P2Exp6
getADimension() - Method in class etomica.potential.P2Exp6Buckingham
getAdjustInterval() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
getAdjustInterval() - Method in class etomica.overlap.IntegratorOverlap
getAdjustStepSize() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
getAelement() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
getAgent(IAtom) - Method in class etomica.atom.AtomLeafAgentManager: Returns the agent associated with the given IAtom.
getAgent(IAtomType) - Method in class etomica.atom.AtomTypeAgentManager: Convenience method to return the agent the given AtomType.
getAgent(IMolecule) - Method in class etomica.atom.MoleculeAgentManager: Returns the agent associated with the given IAtom.
getAgent(ISpecies) - Method in class etomica.atom.SpeciesAgentManager: Convenience method to return the agent the given AtomType.
getAgent(IBox) - Method in class etomica.box.BoxAgentManager: Returns the agent associated with the given box
getAgentClass() - Method in class etomica.dimer.IntegratorEnergyMap
getAgentClass() - Method in class etomica.graphics.BondListener
getAgentClass() - Method in class etomica.graphics.ColorSchemeCollectiveAgent
getAgentClass() - Method in class etomica.graphics.ColorSchemeRandom
getAgentClass() - Method in class etomica.integrator.IntegratorRigidIterative
getAgentClass() - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
getAgentClass() - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
getAgentManager() - Method in class etomica.integrator.IntegratorVelocityVerlet
getAgentManager() - Method in class etomica.modules.catalysis.InteractionTracker
getAgentManager() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
getAgentManager() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
getAgentManager() - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
getAgentManager() - Method in class etomica.normalmode.HSNPT.ActionSummer
getAlertMessage() - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
getAlertMsgBoxController() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
getAlertMsgBoxSpeciesRemoval() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getAlign(int) - Method in class etomica.graphics.DisplayBox
getAlign(int) - Method in class etomica.graphics.DisplayPolytope
getAlkaneIndex() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getAlkaneIndex() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getAlkaneLength(int) - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
getAlkaneLengthSelectionDM() - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
getAlkaneLengthSelectionView(int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
getAlkaneSpheresSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getAllActions() - Method in interface etomica.action.ActionGroup: Returns all actions from this group.
getAllActions() - Method in class etomica.action.ActionGroupSeries
getAllActions() - Method in class etomica.action.activity.ActivityGroupParallel
getAllActions() - Method in class etomica.action.activity.ActivityGroupSeries
getAllListeners() - Method in class etomica.listener.IntegratorListenerGroupSeries
getAllListeners() - Method in interface etomica.listener.ListenerGroup: Returns all actions from this group.
getAllMyData() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
getAllMyData() - Method in class etomica.virial.MeterVirialBinMultiThreaded
getAllMyData() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
getAllowedScriptTypes() - Method in class etomica.graph.view.rasterizer.SVGConverter: Returns the list of allowed script types.
getAllQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
getAllQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
getAlpha() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
getAlpha() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
getAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getAlpha() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
getAlpha() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
getAlpha() - Method in class etomica.normalmode.MCMoveHarmonicEin
getAlpha(int) - Method in class etomica.normalmode.MeterOverlapSwitch
getAlpha(int) - Method in class etomica.normalmode.MeterTargetTP
getAlpha(int) - Method in interface etomica.overlap.AlphaSource: Returns the ith alpha value (i=0..(n-1))
getAlpha(int) - Method in class etomica.overlap.MeterOverlap
getAlpha() - Method in class etomica.potential.P2Dreiding
getAlpha() - Method in class etomica.potential.P2Exp6Buckingham
getAlpha(int) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap: Returns ith factor used in the overlap value.
getAlphaCarbonType() - Method in class etomica.models.rowley.SpeciesEthanol
getAlphaCarbonType() - Method in class etomica.models.rowley.SpeciesMethanol
getAlphaCenter() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getAlphaCenter() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
getAlphaCenter() - Method in class etomica.normalmode.SimOverlapModule
getAlphaCenter() - Method in class etomica.overlap.MeterOverlap
getAlphaCenter() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
getAlphaCenter() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
getAlphaFac() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
getAlphaHydrogenType() - Method in class etomica.models.rowley.SpeciesEthanol
getAlphaHydrogenType() - Method in class etomica.models.rowley.SpeciesMethanol
getAlphaSource() - Method in class etomica.overlap.DataOverlap: Returns an object capable of returning the different alpha values being used.
getAlphaSource() - Method in class etomica.virial.overlap.DataVirialOverlap
getAlphaSpan() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getAlphaSpan() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
getAlphaSpan() - Method in class etomica.overlap.MeterOverlap
getAlphaSpan() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
getAlphaSpan() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
getAlternateStylesheet() - Method in class etomica.graph.view.rasterizer.SVGConverter
getAlterSimEnv() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getAlterSimEnv() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getAmbientPercent() - Static method in class org.jmol.util.GData
getAminoAcidValenceAndCharge(String, String, int[]) - Static method in class org.jmol.viewer.JmolConstants: returns an array if we have special hybridization or charge
getAmplitude() - Method in class etomica.potential.P2Fene
getAmplitudeDimension() - Method in class etomica.potential.P2Fene: Not implemented correctly.
getAngle(int) - Method in class etomica.config.ConformationChainLinear
getAngle(int) - Method in class etomica.config.ConformationLinear
getAngle() - Method in class etomica.math.Quaternion: Returns the angle associated with the quaternion
getAngle() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getAngle() - Method in class etomica.potential.P3BondAngle: Returns the nominal bond angle (in radians)
getAngle() - Method in class etomica.potential.P3BondAngleDreiding: Returns the nominal bond angle (in radians)
getAngle() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig: Returns the nominal bond angle (in radians)
getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveCubic
getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveCubic
getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
getAngleDimension() - Method in class etomica.potential.P3BondAngle
getAngleDimension() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveCubic
getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
getAngles() - Method in class etomica.potential.P2WaterPotentialsJankowski
getAngstromDepth() - Method in class g3dsys.control.G3DSys: Gets the Angstrom depth of the model
getAngstromHeight() - Method in class g3dsys.control.G3DSys: Gets the Angstrom height of the model
getAngstromWidth() - Method in class g3dsys.control.G3DSys: Gets the Angstrom width of the model
getAngularVelocity() - Method in class etomica.atom.AtomOrientedDynamic
getAngularVelocity() - Method in interface etomica.atom.IAtomOrientedKinetic
getAngularVelocity() - Method in interface etomica.atom.IMoleculeOrientedKinetic
getAngularVelocity() - Method in class etomica.atom.MoleculeOrientedDynamic
getAnharmonicConstant() - Method in class etomica.potential.P2Anharmonic
getAnharmonicConstantDimension() - Method in class etomica.potential.P2Anharmonic
getAPair(int, int) - Method in class etomica.virial.AtomPairSet: Returns atom pair for ith and jth atoms in set.
getAPairSet() - Method in class etomica.virial.BoxCluster
getApi1A() - Method in class etomica.atom.iterator.MpiMolecule: Returns the 1A iterator set at construction.
getApiAA() - Method in class etomica.atom.iterator.MpiMolecule: Returns the AA iterator set at construction.
getApproximation() - Method in class etomica.virial.cluster.ClusterOperations
getArea() - Method in class etomica.graph.view.rasterizer.SVGConverter
getArea() - Method in class etomica.math.geometry.Parallelogram
getArea() - Method in class etomica.math.geometry.Polygon
getArea() - Method in class etomica.math.geometry.PolygonGeneral: Returns the value of the area enclosed by the polygon
getArea() - Method in class etomica.math.geometry.Rectangle: Returns the area enclosed by the rectangle.
getArea() - Method in class etomica.math.geometry.Square: Returns edgeLength^2.
getArgb(short) - Static method in class org.jmol.util.Colix
getArgb() - Method in class org.jmol.util.Rgb16
getArgbFromString(String) - Static method in class org.jmol.util.ColorUtil: accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or [red,green,blue] or a valid JavaScript color
getArgbGreyscale(short) - Static method in class org.jmol.util.Colix
getArray() - Method in class etomica.atom.AtomsetArray
getArray() - Method in class etomica.atom.MoleculesetArray
getArrayDimension() - Method in class etomica.data.types.DataDoubleArray: Returns the dimension of the array, which is the number of integer indices needed to access one of its elements.
getArrayDimension() - Method in class etomica.data.types.DataDoubleBDArray: Returns the dimension of the array, which is the number of integer indices needed to access one of its elements.
getArrayList() - Method in class etomica.atom.AtomListWrapper
getArrayList() - Method in class etomica.atom.MoleculeListWrapper
getArrayListPotentialCollection() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
getArrayShape() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray: Returns the size of each dimension in the constructed DataDoubleArray.
getArrayShape() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory: Returns a copy of the array shape array.
getArrayShape(int) - Method in class etomica.data.types.DataDoubleArray: Returns the length of the array in the i-th dimension.
getArrayShape() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray: Returns the size of each dimension in the constructed DataDoubleArray.
getArrayShape() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory: Returns a copy of the array shape array.
getArrayShape(int) - Method in class etomica.data.types.DataDoubleBDArray: Returns the length of the array in the i-th dimension.
getArticulationPair() - Method in class etomica.graph.property.FFTDecomposition
getArticulationPair() - Method in class etomica.graph.property.IsFFT
getArticulationPoints() - Method in class etomica.graph.property.HasSimpleArticulationPoint
getAscent() - Method in class org.jmol.util.JmolFont
getAspect() - Method in class g3dsys.images.Ellipse: set the aspect ratio (y/x) of the figure
getAssociatedAtoms() - Method in class etomica.association.AssociationManager
getAssociatedAtoms(IAtom) - Method in class etomica.association.AssociationManager: Returns the number of atoms on the list of associations of the given atom.
getAssociatedMolecules() - Method in class etomica.association.AssociationManagerMolecule
getAssociatedMolecules(IMolecule) - Method in class etomica.association.AssociationManagerMolecule: Returns the number of atoms on the list of associations of the given atom.
getAssociationDefinition() - Method in class etomica.association.AssociationManager
getAssociationDefinition() - Method in class etomica.association.AssociationManagerMolecule
getAsText() - Method in class etomica.graphics.DimensionedDoubleEditor: Returns the value in the editor's units, formatted as a text string.
getAtom(int) - Method in interface etomica.api.IAtomList: Returns the i-th atom, with numbering beginning from 0.
getAtom() - Method in interface etomica.api.IBoxAtomEvent
getAtom() - Method in class etomica.association.AtomSourceRandomDimer
getAtom() - Method in class etomica.association.AtomSourceRandomMonomer
getAtom() - Method in class etomica.association.AtomSourceRandomSmer
getAtom(int) - Method in class etomica.atom.AtomArrayList
getAtom(int) - Method in class etomica.atom.AtomListWrapper: Part of implementation of AtomSet interface.
getAtom(int) - Method in class etomica.atom.AtomPair
getAtom(int) - Method in class etomica.atom.AtomsetArray: Part of implementation of AtomSet interface.
getAtom(int) - Method in class etomica.atom.AtomSetSinglet
getAtom() - Method in interface etomica.atom.AtomSource: Returns an atom.
getAtom() - Method in class etomica.atom.AtomSourceRandomLeaf: returns a random atom from the box's leaf atom list
getAtom() - Method in class etomica.atom.AtomSourceRandomSpecies: returns a random atom from the box's leaf atom list
getAtom() - Method in class etomica.atom.iterator.AtomIteratorSinglet
getAtom() - Method in class etomica.box.BoxAtomEvent
getAtom() - Method in class etomica.graphics.ColorSchemeNeighbor
getAtom() - Method in class etomica.graphics.ColorSchemeNeighborCell
getAtom() - Method in class etomica.nbr.site.AtomSite
getAtom() - Method in class etomica.potential.PotentialReactive.BondChangeData
getAtom_aC_A() - Method in class etomica.action.IntegratorDimerApproach
getAtom_aC_B() - Method in class etomica.action.IntegratorDimerApproach
getAtom_aH_A() - Method in class etomica.action.IntegratorDimerApproach
getAtom_aH_B() - Method in class etomica.action.IntegratorDimerApproach
getAtom_H1_A() - Method in class etomica.action.IntegratorDimerApproach
getAtom_O_A() - Method in class etomica.action.IntegratorDimerApproach
getAtom_O_B() - Method in class etomica.action.IntegratorDimerApproach
getAtomAction() - Method in class etomica.action.MoleculeChildAtomAction
getAtomAgentManager() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
getAtomColor(IAtom) - Method in class etomica.association.ColorSchemeSmer
getAtomColor(IAtom) - Method in class etomica.association.ColorSchemeSmerByLength
getAtomColor(IAtom) - Method in class etomica.graphics.ColorScheme
getAtomColor(IAtom) - Method in class etomica.graphics.ColorScheme.Simple
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeByType
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeCell
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeColliders: Applies the special colors to the colliding pair while coloring all other atoms with baseColor.
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeNull: Return without changing atom's color.
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeRandom
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeTemperature
getAtomColor(IAtom) - Method in class etomica.modules.catalysis.ColorSchemeRadical
getAtomColor(IAtom) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
getAtomColor(IAtom) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
getAtomColor(IAtom) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
getAtomColor(IAtom) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
getAtomColor(IAtom) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
getAtomColor(IAtom) - Method in class etomica.modules.materialfracture.StrainColorScheme
getAtomColor(IAtom) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
getAtomCount() - Method in interface etomica.api.IAtomList
getAtomCount() - Method in class etomica.atom.AtomArrayList
getAtomCount() - Method in class etomica.atom.AtomListWrapper: Returns the length of the wrapped array.
getAtomCount() - Method in class etomica.atom.AtomPair
getAtomCount() - Method in class etomica.atom.AtomsetArray: Returns the length of the wrapped array.
getAtomCount() - Method in class etomica.atom.AtomSetSinglet
getAtomDataInfo() - Method in interface etomica.data.DataSourceAtomic
getAtomDataInfo() - Method in class etomica.data.DataSourceRmsVelocity
getAtomDataInfo() - Method in class etomica.data.meter.MeterTensorVelocity
getAtomFilter() - Method in class etomica.graphics.DisplayBox: Accessor method for the atom filter that determines which atoms are displayed.
getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
getAtomicMass(int) - Static method in class org.jmol.util.Elements
getAtomicNumber() - Method in class etomica.chem.elements.ElementChemical
getAtomicNumberDimension() - Method in class etomica.chem.elements.ElementChemical
getAtomLeaf1(IBox) - Static method in class etomica.util.Debug: Returns an AtomPair containing the two atoms with global indices ATOM1_INDEX and ATOM2_INDEX within the given box.
getAtomList(IAtom) - Method in interface etomica.atom.AtomToAtomLeafList: Returns the ArrayList that this instance associates with the given atom.
getAtomList(IAtom) - Method in class etomica.atom.AtomToAtomSetFixed
getAtomList(IAtom) - Method in class etomica.atom.AtomToParentChildList
getAtomPositionDefinition() - Method in class etomica.action.MoleculeActionTranslateTo
getAtomPositionDefinition() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
getAtomPropertiesLike(String) - Static method in class org.jmol.script.Token
getAtoms(IBox) - Static method in class etomica.util.Debug: Returns an AtomPair containing the two atoms with global indices ATOM1_INDEX and ATOM2_INDEX within the given box.
getAtomSource() - Method in class etomica.association.MCMoveDimer
getAtomSource() - Method in class etomica.association.MCMoveDimerRotate
getAtomSource() - Method in class etomica.association.MCMoveSmer
getAtomSource() - Method in class etomica.association.MCMoveSmerRotate
getAtomSource() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
getAtomSource() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveAtom
getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveDimer
getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveMolecule
getAtomSource() - Method in class etomica.models.hexane.MCMoveReptate
getAtomSource() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
getAtomSource() - Method in class etomica.normalmode.MCMoveAtomCoupled
getAtomSource() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
getAtomSource() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getAtomSource() - Method in class etomica.virial.MCMoveClusterAngleBend
getAtomSource() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
getAtomSource() - Method in class etomica.virial.MCMoveClusterAtomQ
getAtomType() - Method in interface etomica.api.ISimulationAtomTypeEvent
getAtomType(int) - Method in interface etomica.api.ISpecies: Returns the child types of this group for the specified index.
getAtomType() - Method in class etomica.simulation.SimulationAtomTypeEvent
getAtomType(int) - Method in class etomica.species.Species
getAtomTypeCount() - Method in interface etomica.api.ISpecies: Returns the number of child types of this group.
getAtomTypeCount() - Method in class etomica.species.Species
getAtomTypes(IPotential) - Method in class etomica.potential.PotentialGroup: Returns the AtomTypes that the given potential applies to if the given potential is within this potential group.
getAverage(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapAvg
getAverage(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getAverage(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
getAverage(int) - Method in class etomica.overlap.DataOverlap: Returns the ratio of the reference to target overlap ratio reference/target for the given value alpha.
getAverage(int) - Method in class etomica.virial.overlap.DataSourceVirialOverlap: Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the given value of the Bennet parameter.
getAverageAndError(int, double, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
getAverageAndError(double) - Method in class etomica.overlap.DataOverlap: Returns the average ratio and its uncertainty for the given value of alpha
getAverageAndError(boolean, double) - Method in class etomica.overlap.DataOverlap: Returns the average from the reference or target system (as specified) and its uncertainty for the given value of alpha
getAverageAndError(int, double, boolean) - Method in class etomica.overlap.DataOverlap
getAverageAndError() - Method in class etomica.virial.overlap.DataVirialOverlap: Returns the total result (appropriate ratio of target, reference and overlap averages) and the uncertainty on that value.
getAverageAndError(int) - Method in class etomica.virial.overlap.DataVirialOverlap
getAverageAntibiasedLogs() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB: Returns the average natural logs of the block averages, for all block sizes.
getAverageAtomPoint() - Method in class g3dsys.control.G3DSys
getAverageLogs() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Returns the average natural logs of the block averages, for all block sizes.
getAverages() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Returns the averages for all block sizes
getAvg() - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
getAvg(int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
getAvgBondLength(double) - Static method in class etomica.atom.AtomHydrogen
getAvgDouble() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
getAxesForEllipsoid(double[], Vector3f[], float[]) - Static method in class org.jmol.util.Quadric
getAxis() - Method in class etomica.math.Quaternion: Returns the axis associated with the Quaternion.
getB() - Method in class etomica.association.MCMoveBiasUB
getB() - Method in class etomica.association.MCMoveBiasUBMolecule
getB() - Method in class etomica.association.MCMoveDimer: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.association.MCMoveDimerRotate: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.association.MCMoveSmer: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.association.MCMoveSmerRotate: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.association.MCMoveVolumeAssociated
getB() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
getB() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.freeenergy.npath.MCMoveAtomNPath
getB() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
getB() - Method in class etomica.integrator.mcmove.MCMove: Returns the temperature-dependent part of the acceptance probability.
getB() - Method in class etomica.integrator.mcmove.MCMoveAtom: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
getB() - Method in class etomica.integrator.mcmove.MCMoveDimer: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
getB() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
getB() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
getB() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
getB() - Method in class etomica.integrator.mcmove.MCMoveMolecule: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
getB() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
getB() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
getB() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
getB() - Method in class etomica.integrator.mcmove.MCMoveVolume
getB() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
getB() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
getB() - Method in class etomica.math.geometry.Plane
getB() - Method in class etomica.models.hexane.MCMoveCBMC
getB() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
getB() - Method in class etomica.models.hexane.MCMoveReptate
getB() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
getB() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
getB() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
getB() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
getB() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
getB() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
getB() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
getB() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
getB() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
getB() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
getB() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
getB() - Method in class etomica.modules.pistoncylinder.PistonPlane
getB() - Method in class etomica.modules.rheology.IntegratorPolymer
getB() - Method in class etomica.modules.sam.P1Sinusoidal
getB() - Method in class etomica.modules.sam.WallPlane
getB() - Method in class etomica.normalmode.MCMoveAtomCoupled
getB() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.normalmode.MCMoveAtomSuperBox: Returns the log of the limiting-distribution probabilities of states, ln(Pj/Pi), for the states encountered before (i) and after (j) the most recent call to doTrial.
getB() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
getB() - Method in class etomica.normalmode.MCMoveHarmonic
getB() - Method in class etomica.normalmode.MCMoveHarmonicStep
getB() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
getB() - Method in class etomica.normalmode.MCMovePhaseAngle
getB() - Method in class etomica.normalmode.MCMoveSingleMode
getB() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
getB() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
getB() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
getB() - Method in class etomica.normalmode.MCMoveVolumeSolid
getB() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
getB() - Method in class etomica.normalmode.MCMoveWV
getB() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
getB() - Method in class etomica.potential.P2Exp6
getB() - Method in class etomica.spin.MCMoveSpinFlip
getB() - Method in class etomica.util.numerical.PadeApproximation
getB(int) - Method in class etomica.virial.cluster.ClusterOperations
getB() - Method in class etomica.virial.MCMoveChangeBondLength
getB() - Method in class etomica.virial.MCMoveClusterAngleBend
getB() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
getB() - Method in class etomica.virial.MCMoveClusterAtom
getB() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
getB() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
getB() - Method in class etomica.virial.MCMoveClusterAtomHSChain
getB() - Method in class etomica.virial.MCMoveClusterAtomHSRing
getB() - Method in class etomica.virial.MCMoveClusterAtomHSTree
getB() - Method in class etomica.virial.MCMoveClusterAtomMulti
getB() - Method in class etomica.virial.MCMoveClusterAtomQ
getB() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
getB() - Method in class etomica.virial.MCMoveClusterDiagram
getB() - Method in class etomica.virial.MCMoveClusterMolecule
getB() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
getB() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
getB() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
getB() - Method in class etomica.virial.MCMoveClusterReptateMulti
getB() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
getB() - Method in class etomica.virial.MCMoveClusterRingRegrow
getB() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
getB() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
getB() - Method in class etomica.virial.MCMoveClusterRingScale
getB() - Method in class etomica.virial.MCMoveClusterRotateCH3
getB() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
getB() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
getB() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
getB() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
getB() - Method in class etomica.virial.MCMoveClusterTorsionMulti
getB() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
getB() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
getB() - Method in class etomica.virial.MCMoveClusterWiggleMulti
getB() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
getBackgroundColor() - Method in class etomica.graph.view.rasterizer.SVGConverter
getBackgroundColor() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Gets the background color of the display box canvas.
getBackgroundColor() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Gets the background color of the display box canvas.
getBarrier() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getBarrier() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getBarrier() - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
getBarrierDimension() - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
getBasis() - Method in class etomica.lattice.BravaisLatticeCrystal
getBasis() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
getBasis() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
getBasis() - Method in class etomica.normalmode.CoordinateDefinition
getBasisCells() - Method in class etomica.normalmode.CoordinateDefinition
getBasisMolecules() - Method in class etomica.modules.sam.ConfigurationSAM
getBasisSize() - Method in class etomica.lattice.LatticeCubicSimple: Returns 1.
getBasisSurface() - Method in class etomica.modules.sam.ConfigurationSAM
getBboxVertices() - Method in class org.jmol.util.BoxInfo
getBDimension() - Method in class etomica.potential.P2Exp6
getBDimension() - Method in class etomica.potential.P2Exp6Buckingham
getBennetAverage(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: Returns average value of expression used to determine optimal Bennet parameter (value[1]/(value[1]+expX[iParam]).
getBennetBias(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2: Returns iParam'th factor used in the Bennet sum.
getBennetBias(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: Returns iParam'th factor used in the Bennet sum.
getBeta() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
getBeta() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
getBeta() - Method in class etomica.potential.P4TorsionDreiding
getBetaUAWf() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getBetaUAWf() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getBetaUAWr() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getBetaUAWr() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getBetaUBWf() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getBetaUBWf() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getBetaUBWr() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getBetaUBWr() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getBgColixes(short[]) - Method in class org.jmol.util.GData
getBiasCubeDimensions() - Method in class etomica.association.BiasVolumeCube
getBiasSphereRadius() - Method in class etomica.association.BiasVolume2SiteAceticAcid
getBiasSphereRadius() - Method in class etomica.association.BiasVolumeAceticAcid
getBiasSphereRadius() - Method in class etomica.association.BiasVolumeSphere
getBiasSphereRadius() - Method in class etomica.association.BiasVolumeSphereOriented
getBiasSphereRadius() - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
getBiComponents(Graph) - Static method in class etomica.graph.traversal.BCVisitor: Returns the biconnected components of the given graph.
getBinCounts() - Method in class etomica.util.HistogramSimple
getBinSize() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
getBisectingPlane(Point3f, Vector3f, Point3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
getBitSet(ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
getBlockCount() - Method in class etomica.data.AccumulatorAverage: Returns the number of blocks that have been accumulated since construction or the last call to reset.
getBlockDataSink() - Method in class etomica.data.AccumulatorAverageFixed
getBlockingSet(Graph) - Method in class etomica.graph.iterators.filters.GlobalFilter
getBlockSize() - Method in class etomica.data.AccumulatorAverage: Returns the current value of the block size.
getBn(double, double[], double[]) - Static method in class etomica.virial.BnJHBVArgon_Analytic
getBond(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
getBond(int) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
getBond(int) - Method in class etomica.virial.cluster.ClusterTreeNode
getBondAngle() - Method in class etomica.models.hexane.SpeciesHexane
getBondChangeData() - Method in interface etomica.potential.PotentialReactive
getBondConstratins(ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
getBondDelta() - Method in class etomica.potential.P2HardBond: Accessor method for the bond extension factor
getBondDelta() - Method in class etomica.potential.P2PenetrableBond: Accessor method for the bond extension factor
getBondedList(IAtom) - Method in class etomica.potential.P2HardBondedList: Returns the list containing the bonds for the given atom.
getBondFac() - Method in class etomica.modules.colloid.P2HardSphereMC
getBondFac() - Method in class etomica.modules.colloid.P2SquareWellMonomer
getBondIndexArray() - Method in class etomica.virial.ClusterBonds
getBondingPotential() - Method in class etomica.chem.models.ModelChain: Returns the bonding potential used for adjacent atoms in the chain molecule.
getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
getBondingRadiusFloat(short, int) - Static method in class org.jmol.util.Elements
getBondL() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getBondL() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getBondL() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getBondL() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getBondL() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getBondL() - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
getBondL() - Method in class etomica.virial.SpeciesFactorySpheres2
getBondLength() - Method in class etomica.atom.AtomHydrogen
getBondLength() - Method in class etomica.config.ConformationChainLinear
getBondLength() - Method in class etomica.config.ConformationLinear
getBondlength() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
getBondLength() - Method in class etomica.models.hexane.SpeciesHexane
getBondLength() - Method in class etomica.potential.P2Dreiding
getBondLength() - Method in class etomica.potential.P2HardBond: Accessor method for the bond length
getBondLength() - Method in class etomica.potential.P2PenetrableBond: Accessor method for the bond length
getBondLength() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getBondLength() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getBondLength() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getBondLengthDimension() - Method in class etomica.config.ConformationChainLinear
getBondLengthDimension() - Method in class etomica.config.ConformationLinear
getBondLengthDimension() - Method in class etomica.potential.P2HardBond
getBondLengthDimension() - Method in class etomica.potential.P2PenetrableBond
getBondLengths() - Method in class etomica.potential.P2WaterPotentialsJankowski
getBondsTree() - Method in class etomica.virial.ClusterTree
getBondTheta() - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
getBondTheta() - Method in class etomica.virial.SpeciesFactorySpheres2
getBondType() - Method in class g3dsys.images.Bond
getBoolean() - Method in class etomica.integrator.IntegratorGear4NPH.EnsembleToggler
getBoolean() - Method in interface etomica.modifier.ModifierBoolean: Returns the current state of the modified value.
getBoolean() - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
getBoolean(boolean) - Static method in class org.jmol.script.ScriptVariable
getBoundaries() - Method in class etomica.modules.rosmosis.MeterFlux
getBoundary() - Method in interface etomica.api.IBoundaryEvent
getBoundary() - Method in interface etomica.api.IBox: Returns the box's boundary.
getBoundary() - Method in class etomica.box.Box
getBoundary() - Method in class etomica.space.BoundaryEvent
getBoundaryFrameColor() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Gets the color of box boundary.
getBoundaryFrameColor() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Gets the color of box boundary.
getBoundaryPadding() - Method in class etomica.config.ConfigurationLattice
getBoundaryTensor() - Method in class etomica.space.BoundaryDeformablePeriodic: Returns the boundary tensor that fully describes the shape of the boundary.
getBoundaryVectors() - Method in class g3dsys.control.G3DSys: Gets the boundary vectors used for calculating image shells
getBoundaryVectors() - Method in class g3dsys.images.ImageShell
getBoundaryVectorsIterator() - Method in class g3dsys.control.G3DSys: Gets the index iterator used for calculating image shells
getBoundaryVectorsIterator() - Method in class g3dsys.images.ImageShell
getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
getBoundBoxInfo() - Method in class org.jmol.util.BoxInfo
getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
getBoundingBoxCenter() - Method in class g3dsys.control.G3DSys
getBox() - Method in interface etomica.action.BoxAction
getBox() - Method in class etomica.action.BoxActionAdapter
getBox() - Method in class etomica.action.BoxRandomizeMomenta
getBox() - Method in class etomica.action.BoxScaleMomenta
getBox() - Method in class etomica.action.WriteConfiguration: Returns the box whose atom coordinates get written to the file.
getBox() - Method in class etomica.action.WriteConfigurationBinary: Returns the box whose atom coordinates get written to the file.
getBox() - Method in class etomica.action.WriteConfigurationDLPOLY: Returns the box whose atom coordinates get written to the file.
getBox() - Method in class etomica.action.WriteConfigurationP2DLPOLY: Returns the box whose atom coordinates get written to the file.
getBox() - Method in interface etomica.api.IBoundary: Returns the boundary's IBox.
getBox() - Method in interface etomica.api.IBoxEvent
getBox(int) - Method in interface etomica.api.ISimulation: Returns Box specified by index contained in the Simulation
getBox() - Method in interface etomica.api.ISimulationBoxEvent
getBox() - Method in class etomica.association.MeterDimerMoleFraction
getBox() - Method in class etomica.atom.AtomLeafAgentManager: Convenience method to return the box the Manager is tracking.
getBox() - Method in class etomica.atom.MoleculeAgentManager: Convenience method to return the box the Manager is tracking.
getBox() - Method in class etomica.box.BoxEvent
getBox() - Method in class etomica.data.DataProcessorInterfacialTension
getBox() - Method in class etomica.data.meter.MeterAvgBondLength
getBox() - Method in class etomica.data.meter.MeterBondOrderParameterQ
getBox() - Method in class etomica.data.meter.MeterDensity
getBox() - Method in class etomica.data.meter.MeterDihedralAngle
getBox() - Method in class etomica.data.meter.MeterDipoleSumSquared1site
getBox() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
getBox() - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
getBox() - Method in class etomica.data.meter.MeterKineticEnergy
getBox() - Method in class etomica.data.meter.MeterKineticEnergyRigid
getBox() - Method in class etomica.data.meter.MeterLocalMoleFraction
getBox() - Method in class etomica.data.meter.MeterMoleFraction
getBox() - Method in class etomica.data.meter.MeterMomentumCOM
getBox() - Method in class etomica.data.meter.MeterNMolecules
getBox() - Method in class etomica.data.meter.MeterPositionCOM
getBox() - Method in class etomica.data.meter.MeterPotentialEnergy
getBox() - Method in class etomica.data.meter.MeterPressureTensor: Returns the integrator associated with this instance.
getBox() - Method in class etomica.data.meter.MeterProfile
getBox() - Method in class etomica.data.meter.MeterProfileByAtoms
getBox() - Method in class etomica.data.meter.MeterProfileByVolume
getBox() - Method in class etomica.data.meter.MeterRadiusGyration
getBox() - Method in class etomica.data.meter.MeterRDF
getBox() - Method in class etomica.data.meter.MeterRDFPC
getBox() - Method in class etomica.data.meter.MeterTensorVelocity
getBox() - Method in class etomica.data.meter.MeterVolume
getBox() - Method in class etomica.graphics.DeviceNSelector
getBox() - Method in class etomica.graphics.DisplayBox
getBox() - Method in class etomica.integrator.IntegratorBox
getBox() - Method in class etomica.integrator.mcmove.MCMoveBox
getBox() - Method in class etomica.integrator.mcmove.MCMoveManager
getBox() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
getBox() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
getBox() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
getBox() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
getBox() - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
getBox() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getBox() - Method in class etomica.modules.dcvgcmd.MeterFlux
getBox() - Method in class etomica.modules.droplet.MeterDeformation
getBox() - Method in class etomica.modules.entropylottery.MeterEntropy
getBox() - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
getBox() - Method in class etomica.modules.materialfracture.MeterElongation
getBox() - Method in class etomica.modules.materialfracture.MeterStrain
getBox() - Method in class etomica.modules.materialfracture.MeterStress
getBox() - Method in class etomica.modules.materialfracture.StrainColorScheme
getBox() - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
getBox() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
getBox() - Method in class etomica.modules.rosmosis.MeterFlux
getBox() - Method in class etomica.modules.vle.MeterPressure2
getBox() - Method in class etomica.normalmode.CoordinateDefinition
getBox() - Method in class etomica.normalmode.DeviceCellNum3DSlider
getBox() - Method in class etomica.normalmode.DeviceCellNumXYSlider
getBox() - Method in class etomica.normalmode.MeterAPIPotentialEnergy
getBox() - Method in class etomica.normalmode.MeterAtomicDisplacement
getBox() - Method in class etomica.normalmode.MeterHarmonicEnergy
getBox() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
getBox() - Method in class etomica.normalmode.MeterNormalMode
getBox() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
getBox() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
getBox() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
getBox() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
getBox() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getBox() - Method in class etomica.parser.ParmedStructure: Gets the (single, rectangular) box found in this Structure.
getBox(int) - Method in class etomica.simulation.Simulation: Returns an array of Boxs contained in the Simulation
getBox() - Method in class etomica.simulation.SimulationBoxEvent
getBox() - Method in class etomica.space.Boundary: Returns the boundary's box.
getBox() - Method in class etomica.spin.MeterSpin
getBox() - Method in class etomica.virial.MCMoveClusterAtomQ
getBox() - Method in class etomica.virial.MeterSamplingWeight
getBox() - Method in class etomica.virial.MeterVirial
getBox() - Method in class etomica.virial.MeterVirialBD
getBox() - Method in class etomica.virial.MeterVirialBDBin
getBox() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
getBox() - Method in class etomica.virial.MeterVirialBinMultiThreaded
getBox() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
getBox() - Method in class etomica.virial.MeterVirialExternalField
getBox() - Method in class etomica.virial.MeterVirialExternalFieldConfined
getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
getBox() - Method in class etomica.virial.MeterVirialExternalFieldRho
getBox() - Method in class etomica.virial.MeterVirialExternalFieldSW
getBox() - Method in class etomica.virial.MeterVirialIC
getBox() - Method in class etomica.virial.MeterVirialSWWE
getBoxCount() - Method in interface etomica.api.ISimulation: Returns number of boxes contained in the Simulation
getBoxCount() - Method in class etomica.simulation.Simulation
getBoxFactory() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
getBoxIndex() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getBoxSize() - Method in interface etomica.api.IBoundary: Returns the length of the sides of a rectangular box oriented in the lab frame and in which the boundary is inscribed.
getBoxSize() - Method in class etomica.space.BoundaryDeformablePeriodic: Returns the length of the sides of a rectangular box oriented in the lab frame and in which the boundary is inscribed.
getBoxSize() - Method in class etomica.space.BoundaryRectangular: Returns a vector with elements equal to the lengths of the edges of the boundary.
getBoxSize() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
getButton() - Method in class etomica.graphics.DeviceButton
getBXX() - Method in class etomica.models.rowley.P2RepRowley
getBXXDimension() - Method in class etomica.models.rowley.P2RepRowley
getByte1() - Method in class etomica.graph.engine.impl.BinaryOpByteImpl
getByte1() - Method in class etomica.graph.engine.impl.UnaryOpByteImpl
getByte1() - Method in class etomica.graph.engine.impl.UnaryOpTwoByteImpl
getByte1() - Method in interface etomica.graph.engine.Parser.BinaryOpByte
getByte1() - Method in interface etomica.graph.engine.Parser.UnaryOpByte
getByte1() - Method in interface etomica.graph.engine.Parser.UnaryOpTwoByte
getByte2() - Method in class etomica.graph.engine.impl.UnaryOpTwoByteImpl
getByte2() - Method in interface etomica.graph.engine.Parser.UnaryOpTwoByte
getC() - Method in class etomica.math.geometry.Plane
getC() - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
getC() - Method in class etomica.modules.pistoncylinder.PistonPlane
getC() - Method in class etomica.modules.sam.WallPlane
getC() - Method in class etomica.potential.P2Exp6
getC(int) - Method in class etomica.virial.cluster.ClusterOperations
getC_2Type() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
getC_2Type() - Method in class etomica.virial.SpeciesAlkaneEH
getC_3Type() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
getC_3Type() - Method in class etomica.virial.SpeciesAlkaneEH
getCallCount() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getCallCount() - Method in class etomica.normalmode.MeterNormalMode
getCancelMap() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
getCancelMap() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
getCancelMap() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
getCancelMap() - Method in class etomica.virial.cluster.VirialDiagrams
getCancelMap() - Method in class etomica.virial.cluster.VirialDiagramsMix2
getCancelMap() - Method in class etomica.virial.cluster.VirialDiagramsPT
getCancelMap() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
getCancelMap() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
getCanonicalCopy(float) - Method in class org.jmol.util.BoxInfo
getCanonicalCopy(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
getCapSlabObject(String, boolean) - Static method in class org.jmol.util.MeshSurface: legacy -- for some scripts with early isosurface slabbing
getCarbonType() - Method in class etomica.models.rowley.SpeciesEthanol
getCarbonType() - Method in class etomica.virial.SpeciesTraPPECO2
getCDimension() - Method in class etomica.potential.P2Exp6
getCDimension() - Method in class etomica.potential.P2Exp6Buckingham
getCell(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
getCell(IAtom) - Method in class etomica.nbr.cell.NeighborCellManager
getCellAgentManager() - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
getCellAgentManager() - Method in class etomica.nbr.PotentialMasterNbr
getCellRange() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Returns the cellRange.
getCellRange() - Method in class etomica.nbr.cell.NeighborCellManager: Returns the cellRange.
getCellRange() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
getCellRange() - Method in class etomica.nbr.list.PotentialMasterList
getCellRange() - Method in class etomica.nbr.PotentialMasterHybrid
getCellRange() - Method in class etomica.nbr.site.PotentialMasterSite
getCellSize() - Method in class etomica.lattice.CellLattice: Returns the spatial dimensions of all cells in the lattice, such that a cell in the lattice will have a size in each direction as given by the corresponding value in the returned array.
getCellSizeX() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getCellSizeX() - Method in class etomica.modules.sam.ConfigurationSAM
getCellSizeZ() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getCellSizeZ() - Method in class etomica.modules.sam.ConfigurationSAM
getCenter() - Method in interface etomica.api.IBoundary
getCenter() - Method in class etomica.space.Boundary
getCenterAndPoints(List<Point3f>) - Static method in class org.jmol.util.Measure
getCenterOfRotation() - Method in class g3dsys.control.G3DSys
getCH2element() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
getCH2Type() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
getCH2Type() - Method in class etomica.virial.SpeciesAlkane
getCH3element() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
getCH3Type() - Method in class etomica.models.OPLS.SpeciesAceticAcid
getCH3Type() - Method in class etomica.models.traPPE.SpeciesMethanol
getCH3Type() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
getCH3Type() - Method in class etomica.virial.SpeciesAlkane
getChainlength() - Method in class etomica.models.hexane.MCMoveCBMC
getChainLength() - Method in class etomica.modules.colloid.ColloidSim
getChainLength() - Method in class etomica.modules.colloid.ConfigurationColloid
getChainLength() - Method in class etomica.modules.rheology.SimulationRheology
getChainPhi(int) - Method in class etomica.modules.sam.Sam
getChainPsi() - Method in class etomica.modules.sam.Sam
getChainTheta() - Method in class etomica.modules.sam.Sam
getChangeableColix(short, int) - Method in class org.jmol.util.GData
getChangeableColixIndex(short) - Static method in class org.jmol.util.Colix
getCharge(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getCharge(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getCharge(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getCharge1() - Method in class etomica.potential.P2Electrostatic: Returns the charge on the first type of atom.
getCharge1() - Method in class etomica.potential.P2ElectrostaticWithHardCore: Returns the charge on the first type of atom.
getCharge2() - Method in class etomica.potential.P2Electrostatic: Returns the charge on the second type of atom.
getCharge2() - Method in class etomica.potential.P2ElectrostaticWithHardCore: Returns the charge on the second type of atom.
getChargeH() - Method in class etomica.models.water.P2Water4PSoft
getChargeH() - Method in class etomica.models.water.P2WaterTIP4P
getChargeM() - Method in class etomica.models.water.P2Water4PSoft
getChargeM() - Method in class etomica.models.water.P2WaterTIP4P
getCheckBox() - Method in class etomica.graphics.DeviceCheckBox
getChildCount() - Method in class etomica.species.SpeciesSpheresHetero: Returns the number of child atoms of each type created by this factory.
getChildIndex() - Method in interface etomica.api.IAtomType
getChildIndex() - Method in class etomica.atom.AtomTypeLeaf
getChildList() - Method in interface etomica.api.IMolecule: Returns the atoms in the molecule as an IAtomList.
getChildList() - Method in class etomica.atom.Molecule
getCHType() - Method in class etomica.virial.SpeciesAnthracene3site464
getCHType() - Method in class etomica.virial.SpeciesAnthracene3site545
getCHType() - Method in class etomica.virial.SpeciesPh3site464
getCHType() - Method in class etomica.virial.SpeciesPh3site545
getCHType() - Method in class etomica.virial.SpeciesTraPPEAnthracene
getCHType() - Method in class etomica.virial.SpeciesTraPPENaphthalene
getCHType() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
getClient() - Method in class etomica.simulation.DataStreamHeader
getCliqueCount() - Method in class etomica.virial.ClusterSumHS
getCliqueCount() - Method in interface etomica.virial.ClusterWheatley: Returns number of cliques for the configuration passed to checkConfig
getCliqueCount() - Method in class etomica.virial.ClusterWheatleyHS
getCliqueCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getCliques() - Method in class etomica.virial.ClusterSumHS
getCliques() - Method in interface etomica.virial.ClusterWheatley: Returns an array containing the clique sets for the configuration passed to checkConfig.
getCliques() - Method in class etomica.virial.ClusterWheatleyHS
getCliques() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getCloseWindow() - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
getCloseWindow() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
getCloseWindow() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getCluster() - Method in class etomica.modules.clustergenerator.ClusterPanel
getCluster() - Method in class etomica.virial.MeterVirialExternalField
getCluster() - Method in class etomica.virial.MeterVirialExternalFieldConfined
getCluster() - Method in class etomica.virial.MeterVirialExternalFieldSW
getClusters() - Method in class etomica.virial.ClusterSum
getClusters() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
getClusters() - Method in class etomica.virial.ClusterSumPolarizable
getClusters() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
getClusters() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
getClusters() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
getClusters() - Method in class etomica.virial.ClusterWeightUmbrella
getClusters() - Method in class etomica.virial.MeterVirial
getClusters() - Method in class etomica.virial.MeterVirialBD
getClusters() - Method in class etomica.virial.MeterVirialSWWE
getCoeffAc(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
getCoeffAc(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
getCoefficients() - Method in interface etomica.normalmode.WaveVectorFactory: Returns the coefficients for the wave vectors returned by getWaveVectors.
getCoefficients() - Method in class etomica.normalmode.WaveVectorFactory1D
getCoefficients() - Method in class etomica.normalmode.WaveVectorFactory2D
getCoefficients() - Method in class etomica.normalmode.WaveVectorFactoryFcc
getCoefficients() - Method in class etomica.normalmode.WaveVectorFactoryFromFile
getCoefficients() - Method in class etomica.normalmode.WaveVectorFactorySimple
getColix(Color) - Static method in class g3dsys.control.G3DSys: Converts the given AWT color to a G3D Colix
getColix(int) - Static method in class g3dsys.control.G3DSys: Converts the given argb int to a G3D Colix
getColix(int) - Static method in class org.jmol.util.Colix
getColixArray(String) - Static method in class org.jmol.util.Colix
getColixInherited(short, short) - Static method in class org.jmol.util.Colix
getColixO(Object) - Static method in class org.jmol.util.Colix
getColixS(String) - Static method in class org.jmol.util.Colix
getColixTranslucencyFractional(short) - Static method in class org.jmol.util.Colix
getColixTranslucencyLevel(short) - Static method in class org.jmol.util.Colix
getColixTranslucent(int) - Static method in class org.jmol.util.Colix
getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.Colix
getCollisionCount() - Method in class etomica.integrator.IntegratorHard
getCollisionDiameter() - Method in class etomica.potential.P2HardSphere: Accessor method for collision diameter
getCollisionDiameterDimension() - Method in class etomica.potential.P2HardSphere
getCollisionRadius() - Method in class etomica.modules.osmosis.MeterOsmoticPressure: Returns the collision radius used to calculate the accessible "area".
getCollisionRadius() - Method in class etomica.modules.osmosis.P1HardWall: Distance from the center of the sphere to the boundary at collision.
getCollisionRadius() - Method in class etomica.potential.P1HardBoundary: Distance from the center of the sphere to the boundary at collision.
getCollisionRadius() - Method in class etomica.potential.P1HardMovingBoundary: Distance from the center of the sphere to the boundary at collision.
getCollisionRadiusDimension() - Method in class etomica.modules.osmosis.P1HardWall: Indicates collision radius has dimensions of Length.
getCollisionRadiusDimension() - Method in class etomica.potential.P1HardBoundary: Indicates collision radius has dimensions of Length.
getCollisionRadiusDimension() - Method in class etomica.potential.P1HardMovingBoundary: Indicates collision radius has dimensions of Length.
getColloidSigma() - Method in class etomica.modules.colloid.ColloidSim
getColor() - Method in interface etomica.graph.model.Edge
getColor() - Method in class etomica.graph.model.impl.EdgeImpl
getColor() - Method in class etomica.graph.model.impl.MetadataImpl
getColor() - Method in class etomica.graph.model.impl.NodeImpl
getColor() - Method in interface etomica.graph.model.Metadata
getColor() - Method in interface etomica.graph.model.Node
getColor(IAtomType) - Method in class etomica.graphics.ColorSchemeByType
getColor() - Method in class g3dsys.images.Axes
getColor() - Method in class g3dsys.images.Ball
getColor() - Method in class g3dsys.images.Box
getColor() - Method in class g3dsys.images.Ellipse
getColor() - Method in class g3dsys.images.Line
getColor() - Method in class g3dsys.images.Triangle
getColor1() - Method in class etomica.graph.engine.impl.UnaryOpColorImpl
getColor1() - Method in class etomica.graph.engine.impl.UnaryOpThreeColorImpl
getColor1() - Method in interface etomica.graph.engine.Parser.UnaryOpColor
getColor1() - Method in interface etomica.graph.engine.Parser.UnaryOpThreeColor
getColor1() - Method in class g3dsys.images.Bond
getColor2() - Method in class etomica.graph.engine.impl.UnaryOpThreeColorImpl
getColor2() - Method in interface etomica.graph.engine.Parser.UnaryOpThreeColor
getColor2() - Method in class g3dsys.images.Bond
getColor3() - Method in class etomica.graph.engine.impl.UnaryOpThreeColorImpl
getColor3() - Method in interface etomica.graph.engine.Parser.UnaryOpThreeColor
getColorArgbOrGray(short) - Method in class org.jmol.util.GData
getColorIn() - Method in class etomica.modules.crystalviewer.ColorSchemePlane
getColorMap() - Method in class etomica.graph.engine.impl.UnaryOpByteMapImpl
getColorMap() - Method in interface etomica.graph.engine.Parser.UnaryOpByteMap
getColorOut() - Method in class etomica.modules.crystalviewer.ColorSchemePlane
getColorScheme() - Method in class etomica.graphics.DisplayBox: Accessor method for the color scheme used for this display
getColumn(int, float[]) - Method in class org.jmol.util.Matrix3f: Copies the matrix values in the specified column into the array parameter.
getColumn(int, float[]) - Method in class org.jmol.util.Matrix4f: Copies the matrix values in the specified column into the array parameter.
getColumnClass(int) - Method in class etomica.graphics.DeviceTableModelGeneric
getColumnCount() - Method in class etomica.graphics.DeviceTableModelGeneric: Get the number of columns in the table
getColumnCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
getColumnCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
getColumnCount() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
getColumnInfoFactories() - Method in class etomica.data.types.DataTable.DataInfoTableFactory: Returns a copy of the array of DataInfoFactories for the columns
getColumnName(int) - Method in class etomica.graphics.DeviceTableModelGeneric
getColumnV(int, Vector3f) - Method in class org.jmol.util.Matrix3f: Copies the matrix values in the specified column into the vector parameter.
getCombinationProbability() - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: Returns the probability that two radicals will bond instead of becoming unreactive.
getCommand() - Method in class etomica.graph.engine.impl.CommandImpl
getCommand() - Method in interface etomica.graph.engine.Parser.Command
getCommandSet(String) - Static method in class org.jmol.script.Token: retrieves an unsorted list of viable commands that could be completed by this initial set of characters.
getCompletedActions() - Method in interface etomica.action.activity.ActivityGroup: Returns all actions from this group that have been completed.
getCompletedActions() - Method in class etomica.action.activity.ActivityGroupParallel
getCompletedActions() - Method in class etomica.action.activity.ActivityGroupSeries
getComponent() - Method in class etomica.graphics.DeviceSlider
getComponent() - Method in class etomica.graphics.DeviceSpinner
getComponents(Graph) - Static method in class etomica.graph.traversal.CVisitor: Returns the biconnected components of the given graph.
getComponentValues() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getCOMType() - Method in class etomica.models.water.SpeciesWater4PCOM
getConfigDLPOLY() - Method in class etomica.potential.PotentialDLPOLY
getConfigP2DLPOLY() - Method in class etomica.potential.P2DLPOLY
getConfiguration() - Method in class etomica.action.SimulationRestart
getConfName() - Method in class etomica.action.WriteConfiguration: Returns the configuration name.
getConfName() - Method in class etomica.action.WriteConfigurationBinary: Returns the configuration name.
getConfName() - Method in class etomica.action.WriteConfigurationDLPOLY: Returns the configuration name.
getConfName() - Method in class etomica.action.WriteConfigurationP2DLPOLY: Returns the configuration name.
getConformation() - Method in class etomica.chem.models.ModelChain: Returns the Conformation for the molecule, or null if no Conformation has been set (a ConformationLinear will be used).
getConformation(int) - Method in class etomica.modules.sam.ConfigurationSAM
getConformation() - Method in class etomica.species.Species
getConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getConsole() - Method in interface etomica.graph.engine.ConsoleContainer
getConsole() - Method in class etomica.graph.engine.Launcher.ConsoleWindow
getConstrainScriptOrigin() - Method in class etomica.graph.view.rasterizer.SVGConverter: Returns whether scripts can only be loaded from the same origin as the documents referencing them.
getConstraint() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
getConstraintAngle() - Method in class etomica.models.nitrogen.MeterDirectInitPert
getConstructorObject() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getContainingCubeEdgeLength() - Method in class etomica.math.geometry.TruncatedOctahedron: Returns the length of an edge of a cube in which the truncated octahedron is inscribed.
getController() - Method in class etomica.action.activity.ControllerEvent
getController() - Method in interface etomica.action.ControllerAction
getController() - Method in class etomica.action.ControllerActionAdapter
getController() - Method in class etomica.graphics.Device
getController() - Method in class etomica.graphics.DeviceControllerButton
getController() - Method in class etomica.graphics.SimulationGraphic
getController() - Method in class etomica.normalmode.SimOverlapModule
getController() - Method in class etomica.simulation.Simulation: Returns the Controller used to run the simulation's Actions and Activities.
getControllerButton() - Method in class etomica.graphics.DeviceTrioControllerButton
getConvergence(Potential2SoftSpherical, int, double, double, boolean, boolean) - Static method in class etomica.virial.B3ForSphericallySymmetricU
getConvergence(Potential2SoftSpherical, int, int, double, double, boolean) - Static method in class etomica.virial.BnIETP2Spherical
getConvergence(Potential2SoftSpherical, int, int, double, double, boolean) - Static method in class etomica.virial.BnPY_1QC_Helium
getConvergence(Potential2Spherical, int, double, double, double, boolean, double) - Static method in class etomica.virial.BnPYCHe
getCoordinateDefinition() - Method in class etomica.conjugategradient.DerivativeEnergyFunction
getCoordinateDefinition() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getCoordinateDefinition() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
getCoordinateDefinition() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
getCoordinateDefinition() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
getCoordinateDefinition() - Method in class etomica.normalmode.IntegratorHarmonic
getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveHarmonic
getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveHarmonicStep
getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveSingleMode
getCoordinateDefinition() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getCoordinateDefinition() - Method in class etomica.normalmode.MeterDDP
getCoordinateDefinition() - Method in class etomica.normalmode.MeterDP
getCoordinateDefinition() - Method in class etomica.normalmode.MeterHarmonicCoordinate
getCoordinateDefinition() - Method in class etomica.normalmode.MeterHarmonicEnergy
getCoordinateDefinition() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
getCoordinateDefinition() - Method in class etomica.normalmode.MeterNormalMode
getCoordinateDefinition() - Method in class etomica.normalmode.MeterTargetTP
getCoordinateDefinition() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getCoordinateDefinition() - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
getCoordinateDefinitionParacetamol() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
getCoordinateDim() - Method in class etomica.normalmode.CoordinateDefinition: Returns the number of generalized coordinates associated with each molecule.
getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellBonding: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellSurface: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.modules.mu.P2SquareWellOneSide: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.potential.P2DoubleWell: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.potential.P2PenetrableSphere: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.potential.P2PenetrableSquareWell: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.potential.P2SquareWell: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.potential.P2SquareWellRobust: Accessor method for core diameter.
getCoreDiameter() - Method in class etomica.potential.P2TriangleWell
getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
getCoreDiameterDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
getCoreDiameterDimension() - Method in class etomica.potential.P2DoubleWell
getCoreDiameterDimension() - Method in class etomica.potential.P2PenetrableSphere
getCoreDiameterDimension() - Method in class etomica.potential.P2PenetrableSquareWell
getCoreDiameterDimension() - Method in class etomica.potential.P2SquareWell
getCoreDiameterDimension() - Method in class etomica.potential.P2SquareWellRobust
getCoreDiameterDimension() - Method in class etomica.potential.P2TriangleWell
getCoreEdgeCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
getCoreIterator() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
getCoreLen() - Method in class etomica.graph.isomorphism.AbstractSearchState
getCoreLen() - Method in interface etomica.graph.isomorphism.SearchState
getCoreSet() - Method in class etomica.graph.isomorphism.AbstractSearchState
getCoreSet() - Method in interface etomica.graph.isomorphism.SearchState
getCount() - Method in interface etomica.api.IBoxMoleculeCountEvent
getCount() - Method in class etomica.box.BoxMoleculeCountEvent
getCount() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getCount() - Method in class etomica.normalmode.HSNPT.ActionSummer
getCount() - Method in interface etomica.util.Histogram: Returns the number of times the Histogram's addValue method was called.
getCount() - Method in class etomica.util.HistogramDiscrete
getCount() - Method in class etomica.util.HistogramNotSoSimple
getCount() - Method in class etomica.util.HistogramReweightedData
getCount() - Method in class etomica.util.HistogramSimple
getCountOfMoleculesStrings() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getCountOfSpeciesSLM(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getCountOfSpeciesSLMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getCountSpecies(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getCoupling() - Method in class etomica.spin.P2Spin
getCov(int, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
getCPairID() - Method in class etomica.virial.BoxCluster
getCPairID() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getCPairSet() - Method in class etomica.virial.BoxCluster: returns the current coordinate pair set
getCriteria() - Method in class etomica.potential.PotentialArray
getCriteria() - Method in class etomica.potential.PotentialArrayMolecular
getCriterion(ISpecies) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getCriterion(IPotentialMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Returns the criterion used by to determine what atoms interact with the given potential.
getCriterion(IAtomType) - Method in class etomica.nbr.list.NeighborListManager
getCriterion(IPotentialAtomic) - Method in class etomica.nbr.list.PotentialMasterList: Returns the criterion used by to determine what atoms interact with the given potential.
getCriterion(IPotentialAtomic) - Method in class etomica.nbr.site.PotentialMasterSite: Returns the criterion used by to determine what atoms interact with the given potential.
getCriterion() - Method in class etomica.potential.Potential0
getCriticalPoints(Point3f[], Tuple3f) - Static method in class org.jmol.util.BoxInfo
getCType() - Method in class etomica.AlkaneEH.SpeciesMethane
getCType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
getCType() - Method in class etomica.paracetamol.SpeciesParacetamol
getCType() - Method in class etomica.virial.SpeciesAnthracene3site464
getCType() - Method in class etomica.virial.SpeciesAnthracene3site545
getCType() - Method in class etomica.virial.SpeciesMethane
getCType() - Method in class etomica.virial.SpeciesPh3site464
getCType() - Method in class etomica.virial.SpeciesPh3site545
getCType() - Method in class etomica.virial.SpeciesTraPPEAnthracene
getCType() - Method in class etomica.virial.SpeciesTraPPENaphthalene
getCType() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
getCubicSize() - Method in class etomica.lattice.crystal.PrimitiveBcc: Returns the common length of all primitive vectors.
getCubicSize() - Method in class etomica.lattice.crystal.PrimitiveFcc: Returns the common length of all primitive vectors.
getCurrentActions() - Method in interface etomica.action.activity.ActivityGroup: Returns all actions from this group that are currently being performed.
getCurrentActions() - Method in class etomica.action.activity.ActivityGroupParallel
getCurrentActions() - Method in class etomica.action.activity.ActivityGroupSeries
getCurrentLattice() - Method in class etomica.modules.crystalviewer.LatticeEditor: Returns the currently selected crystal.
getCurrentStep() - Method in class etomica.action.ActionIntegrate
getCurrentStep() - Method in class etomica.action.activity.ActivityIntegrate
getCurrentTime() - Method in class etomica.integrator.IntegratorMD
getCurrentTime() - Method in class etomica.modules.adsorption.IntegratorHybrid
getCurrentTime() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
getCutoff() - Method in class etomica.modules.droplet.AtomFilterLiquid
getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationCone: Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for Lennard-Jones cutoff distance; divided by sigma
getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationCone
getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
getCXX() - Method in class etomica.models.rowley.P2RepRowley
getD() - Method in interface etomica.api.IVector: Dimension of the space occupied by the vector.
getD() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition: Return the block diagonal eigenvalue matrix
getD() - Method in interface etomica.lattice.IndexIterator
getD() - Method in class etomica.lattice.IndexIteratorRectangular: Returns the length of the integer array that is returned as an iterate.
getD() - Method in class etomica.lattice.IndexIteratorReflecting
getD() - Method in class etomica.lattice.IndexIteratorTriangular: Returns the length of the int array that is returned as each iterate.
getD() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
getD() - Method in class etomica.math.discrete.CombinationIterator
getD() - Method in class etomica.math.discrete.PermutationDegenerateIterator
getD() - Method in class etomica.math.discrete.PermutationIterator
getD() - Method in class etomica.math.geometry.Plane
getD() - Method in class etomica.modules.pistoncylinder.PistonPlane
getD() - Method in class etomica.modules.sam.WallPlane
getD(double, double, int) - Method in class etomica.potential.P3CPSNonAdditiveHe
getD(double, double, int) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
getD(double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
getD() - Method in class etomica.space1d.Vector1D
getD() - Method in class etomica.space2d.Vector2D
getD() - Method in class etomica.space3d.Vector3D
getD() - Method in class etomica.spaceNd.VectorND
getD() - Method in interface g3dsys.control.IndexIterator: Get the number of dimensions
getD() - Method in class g3dsys.images.Axes
getD() - Method in class g3dsys.images.Ball
getD() - Method in class g3dsys.images.Bond
getD() - Method in class g3dsys.images.Box
getD() - Method in class g3dsys.images.Ellipse
getD() - Method in class g3dsys.images.ImageShell
getD() - Method in class g3dsys.images.Line
getD2dfac() - Method in class etomica.util.numerical.AkimaSplineSmoother
getD2fac() - Method in class etomica.util.numerical.AkimaSplineSmoother
getD2Sum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
getD3dfac() - Method in class etomica.util.numerical.AkimaSplineSmoother: sets weight given to minimizing discontinuities in the 3nd derivative (at data points)
getD3fac() - Method in class etomica.util.numerical.AkimaSplineSmoother
getDADBSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper: Returns sum of Fi dot ri
getDADBSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut: Returns sum of Fi dot ri
getDADBXYZ() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
getData(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorAverage: This method will return an IData object corresponding to the requested StatType.
getData() - Method in class etomica.data.AccumulatorAverageBlockless: Returns a DataGroup with Data instances holding the statistics kept by this accumulator (as described in general comments for this class).
getData() - Method in class etomica.data.AccumulatorAverageBlocklessSlim: Returns a DataGroup with Data instances holding the statistics kept by this accumulator (as described in general comments for this class).
getData() - Method in class etomica.data.AccumulatorAverageCollapsing: Returns a DataGroup with Data instances holding the statistics kept by this accumulator (as described in general comments for this class).
getData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getData() - Method in class etomica.data.AccumulatorAverageCovariance
getData() - Method in class etomica.data.AccumulatorAverageFixed: Returns a DataGroup with Data instances holding the statistics kept by this accumulator (as described in general comments for this class).
getData() - Method in class etomica.data.AccumulatorAverageFixedOutputFile: Returns a DataGroup with Data instances holding the statistics kept by this accumulator (as described in general comments for this class).
getData() - Method in class etomica.data.AccumulatorCounter: Returns the DataInteger with the count.
getData() - Method in class etomica.data.AccumulatorHistogram: Returns the set of histograms.
getData() - Method in class etomica.data.AccumulatorHistory: Returns the set of histories.
getData() - Method in class etomica.data.AccumulatorRatioAverage
getData() - Method in class etomica.data.AccumulatorRatioAverageCovariance
getData() - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
getData() - Method in class etomica.data.DataAccumulator: Returns the Data generated by accumulating the Data previously given to this instance.
getData() - Method in class etomica.data.DataDump
getData() - Method in class etomica.data.DataSet.DataSetSink
getData(int) - Method in class etomica.data.DataSet: Returns the ith Data from the set.
getData(IAtom) - Method in interface etomica.data.DataSourceAtomic
getData() - Method in class etomica.data.DataSourceFunction: Returns the DataFunction made by this source.
getData() - Method in class etomica.data.DataSourceGroup: Returns a DataGroup that is formed from the Data objects returned by the data sources in this instance.
getData(IMolecule) - Method in interface etomica.data.DataSourceMolecular
getData() - Method in class etomica.data.DataSourcePoints
getData(IVector) - Method in interface etomica.data.DataSourcePositioned
getData(IVector) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
getData() - Method in class etomica.data.DataSourceRmsVelocity: Returns the rms velocity of the atoms given by the iterator.
getData(IAtom) - Method in class etomica.data.DataSourceRmsVelocity
getData() - Method in class etomica.data.DataSourceScalar
getData() - Method in class etomica.data.DataSourceTensorVirialHard: Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
getData() - Method in class etomica.data.DataSourceUniform: Returns the uniformly spaced values.
getData() - Method in class etomica.data.HistogramDataSource: Returns the set of histograms.
getData() - Method in interface etomica.data.IDataSource
getData() - Method in class etomica.data.meter.MeterDihedralAngle: Returns the Dihedral distribution, averaged over the calls to actionPerformed since the meter was reset or had some parameter changed (# of bins).
getData() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
getData() - Method in class etomica.data.meter.MeterHyperVirial: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.data.meter.MeterMomentumCOM: Returns the instantaneous total center-of-mass momentum over all atoms in the box.
getData(IMolecule) - Method in class etomica.data.meter.MeterNMolecules
getData() - Method in class etomica.data.meter.MeterPositionCOM: Returns the position of the center of mass of all atoms in the box.
getData() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
getData() - Method in class etomica.data.meter.MeterPressureByVolumeChange
getData() - Method in class etomica.data.meter.MeterPressureHardTensor
getData() - Method in class etomica.data.meter.MeterPressureTensor: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
getData() - Method in class etomica.data.meter.MeterProfile: Returns the profile for the current configuration.
getData() - Method in class etomica.data.meter.MeterProfileByAtoms: Returns the profile for the current configuration.
getData() - Method in class etomica.data.meter.MeterProfileByVolume: Returns the profile for the current configuration.
getData() - Method in class etomica.data.meter.MeterRDF: Returns the RDF, averaged over the calls to actionPerformed since the meter was reset or had some parameter changed (xMax or # of bins).
getData() - Method in class etomica.data.meter.MeterRDFPC: Returns the RDF, averaged over the calls to actionPerformed since the meter was reset or had some parameter changed (xMax or # of bins).
getData() - Method in class etomica.data.meter.MeterTensorVelocity: Returns the velocity dyad (mass*vv) summed over all atoms, and divided by N
getData(IAtom) - Method in class etomica.data.meter.MeterTensorVelocity: Returns the velocity dyad (mass*vv) for the given atom.
getData() - Method in class etomica.data.types.DataDoubleArray: Returns the encapsulated array.
getData() - Method in class etomica.data.types.DataDoubleBDArray: Returns the encapsulated array.
getData(int) - Method in class etomica.data.types.DataGroup: Returns the i-th data element in the group, counting from 0.
getData() - Method in class etomica.freeenergy.npath.DataSourceEnergies
getData() - Method in class etomica.gaussianwork.MeterBoltzmannA
getData() - Method in class etomica.gaussianwork.MeterBoltzmannB
getData() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getData() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getData() - Method in class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
getData() - Method in class etomica.integrator.IntegratorPT.BoxTracker: Returns array y such that y[i] is the current box of the configuration that began in box i.
getData() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff: Computes total potential energy for box.
getData() - Method in class etomica.liquidLJ.MeterPU: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.liquidLJ.MeterPUCut: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.liquidLJ.MeterPUCutLS
getData() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Performs a Widom insertion average, doing nInsert insertion attempts Temperature used to get exp(-uTest/kT) is that of the integrator for the box
getData() - Method in class etomica.mappedvirial.MeterMeanForce
getData() - Method in class etomica.metastable.MeterDensityDistribution
getData() - Method in class etomica.models.nitrogen.MeterBoltzmann
getData() - Method in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
getData() - Method in class etomica.models.nitrogen.MeterNormalizedCoord: Returns the DataGroup of uDistribtion[i]
getData() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta: Returns the DataGroup of uDistribtion[i]
getData() - Method in class etomica.models.nitrogen.MeterOrientationDistribution: Returns the DataGroup of uDistribtion[i]
getData() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup: Returns the DataGroup of uDistribtion[i]
getData() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getData() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getData() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
getData() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
getData() - Method in class etomica.models.oneDHardRods.MeterOverlap
getData() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
getData() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
getData() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
getData() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
getData() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getData() - Method in class etomica.modules.droplet.MeterDeformation
getData() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
getData() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
getData(IMolecule) - Method in class etomica.modules.interfacial.MeterOrientation
getData() - Method in class etomica.modules.mu.DataSourceWallPressureMu
getData() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getData() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getData() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2: Implements DataSource interface, but you probably want to getData for a specific Bennet parameter.
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getData() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
getData() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getData() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getData() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
getData() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
getData() - Method in class etomica.modules.rosmosis.MeterFlux
getData() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
getData() - Method in class etomica.modules.sam.MeterTilt
getData() - Method in class etomica.normalmode.DataSourceFE
getData() - Method in class etomica.normalmode.DataSourceFEHistogram
getData() - Method in class etomica.normalmode.DataSourceImposedFEFit
getData() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getData() - Method in class etomica.normalmode.DataSourcePMu
getData() - Method in class etomica.normalmode.DataSourcePN
getData() - Method in class etomica.normalmode.MeterAtomicDisplacement
getData() - Method in class etomica.normalmode.MeterBoltzmann
getData() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
getData() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getData() - Method in class etomica.normalmode.MeterBoltzmannTarget: Sets the fraction that the system is coupled to measured energy.
getData() - Method in class etomica.normalmode.MeterDADB
getData() - Method in class etomica.normalmode.MeterDDP
getData() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
getData() - Method in class etomica.normalmode.MeterDirectSamplingTarget
getData() - Method in class etomica.normalmode.MeterDP
getData() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
getData() - Method in class etomica.normalmode.MeterNormalMode: Returns the DataGroup of S(k) Tensors corresponding to the sum of T(k)*transpose(T(-k)).
getData() - Method in class etomica.normalmode.MeterOverlapSwitch
getData() - Method in class etomica.normalmode.MeterPlaneSlip
getData() - Method in class etomica.normalmode.MeterSamplingHarmonic
getData() - Method in class etomica.normalmode.MeterSamplingTarget
getData() - Method in class etomica.normalmode.MeterSolidDA: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.normalmode.MeterSolidDACut: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.normalmode.MeterSolidMirror: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getData() - Method in class etomica.normalmode.MeterSolidProps
getData() - Method in class etomica.normalmode.MeterSolidPropsLJ
getData() - Method in class etomica.normalmode.MeterTargetTP
getData() - Method in class etomica.normalmode.MeterTilt
getData() - Method in class etomica.normalmode.MeterTiltHistogram
getData() - Method in class etomica.normalmode.MeterTiltRotation
getData() - Method in class etomica.normalmode.MeterTiltRotationHistogram
getData() - Method in class etomica.normalmode.MeterTiltRotationStdev
getData() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
getData() - Method in class etomica.normalmode.MeterWorkBennetTarget
getData() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
getData() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
getData() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getData() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
getData() - Method in class etomica.normalmode.MeterWorkTargetBennet
getData() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getData() - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
getData() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
getData() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
getData() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
getData() - Method in class etomica.overlap.MeterOverlap
getData() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
getData() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
getData() - Method in class etomica.potential.P2QChemInterpolated
getData() - Method in class etomica.potential.P3HydrogenManzhos
getData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
getData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
getData() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
getData() - Method in class etomica.virial.MeterSamplingWeight
getData() - Method in class etomica.virial.MeterVirial
getData() - Method in class etomica.virial.MeterVirialBD
getData() - Method in class etomica.virial.MeterVirialExternalField
getData() - Method in class etomica.virial.MeterVirialExternalFieldConfined
getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
getData() - Method in class etomica.virial.MeterVirialExternalFieldRho
getData() - Method in class etomica.virial.MeterVirialExternalFieldSW
getData() - Method in class etomica.virial.MeterVirialIC
getData() - Method in class etomica.virial.MeterVirialSWWE
getData() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: Implements DataSource interface, but you probably want to getData for a specific Bennet parameter.
getData(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: Return all standard data corresponding to the given Bennet parameter.
getDataAsArray() - Method in class etomica.data.meter.MeterMeanSquareDisplacement
getDataAsArray() - Method in class etomica.data.meter.MeterStructureFactor
getDataAsScalar() - Method in class etomica.association.MeterDimerMoleFraction
getDataAsScalar() - Method in class etomica.data.AccumulatorHistory.DataSourceCount
getDataAsScalar() - Method in class etomica.data.DataSourceAcceptanceProbability: Returns the value of the acceptance ratios as currently kept by the MCMove classes identified with setMove.
getDataAsScalar() - Method in class etomica.data.DataSourceAcceptanceRatio: Returns the value of the acceptance ratio as currently kept by the MCMove class identified with setMove.
getDataAsScalar() - Method in class etomica.data.DataSourceAtomDistance
getDataAsScalar() - Method in class etomica.data.DataSourceCountCollisions: Returns the simulation time elapsed by the integrator tracked by this class since the last reset.
getDataAsScalar() - Method in class etomica.data.DataSourceCountSteps: Returns the number of steps performed by the integrator
getDataAsScalar() - Method in class etomica.data.DataSourceCountTime: Returns the simulation time elapsed by the integrator tracked by this class since the last reset.
getDataAsScalar() - Method in class etomica.data.DataSourceScalar: Returns a single scalar value as the measurement for the given box.
getDataAsScalar() - Method in class etomica.data.meter.MeterAvgBondLength
getDataAsScalar() - Method in class etomica.data.meter.MeterBondOrderParameterQ: Returns the value of the bond-order parameter for the given box in its current configuration.
getDataAsScalar() - Method in class etomica.data.meter.MeterDensity
getDataAsScalar() - Method in class etomica.data.meter.MeterDipoleSumSquared1site
getDataAsScalar() - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
getDataAsScalar() - Method in class etomica.data.meter.MeterEnergy: Current value of the total energy (kinetic + potential)
getDataAsScalar() - Method in class etomica.data.meter.MeterKineticEnergy: Returns the total kinetic energy summed over all atoms produced by the iterator when applied to the given box.
getDataAsScalar() - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
getDataAsScalar() - Method in class etomica.data.meter.MeterKineticEnergyRigid: Returns the total kinetic energy summed over all atoms produced by the iterator when applied to the given box.
getDataAsScalar() - Method in class etomica.data.meter.MeterLocalDensity
getDataAsScalar() - Method in class etomica.data.meter.MeterLocalMoleFraction
getDataAsScalar() - Method in class etomica.data.meter.MeterMeanSquareDisplacement
getDataAsScalar() - Method in class etomica.data.meter.MeterMoleFraction
getDataAsScalar() - Method in class etomica.data.meter.MeterNMolecules
getDataAsScalar() - Method in class etomica.data.meter.MeterPotentialEnergy: Computes total potential energy for box.
getDataAsScalar() - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
getDataAsScalar() - Method in class etomica.data.meter.MeterPressure: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getDataAsScalar() - Method in class etomica.data.meter.MeterPressureHard: Returns P = (NT - (virial sum)/((elapsed time)*T*(space dimension)))/V Virial sum and elapsed time apply to period since last call to this method.
getDataAsScalar() - Method in class etomica.data.meter.MeterPressureMolecular: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getDataAsScalar() - Method in class etomica.data.meter.MeterRadiusGyration
getDataAsScalar() - Method in class etomica.data.meter.MeterStructureFactor
getDataAsScalar() - Method in class etomica.data.meter.MeterTemperature
getDataAsScalar() - Method in class etomica.data.meter.MeterVolume
getDataAsScalar() - Method in class etomica.data.meter.MeterWidomInsertion: Performs a Widom insertion average, doing nInsert insertion attempts Temperature used to get exp(-uTest/kT) is that of the integrator for the box
getDataAsScalar() - Method in class etomica.interfacial.MeterWallForce
getDataAsScalar() - Method in class etomica.interfacial.MeterWallPosition
getDataAsScalar() - Method in class etomica.liquidLJ.MeterWidomInsertionP: Performs a Widom insertion average, doing nInsert insertion attempts Temperature used to get exp(-uTest/kT) is that of the integrator for the box
getDataAsScalar() - Method in class etomica.mappedvirial.MeterMappedU
getDataAsScalar() - Method in class etomica.mappedvirial.MeterMappedVirial
getDataAsScalar() - Method in class etomica.mappedvirial.MeterMappedVirialV
getDataAsScalar() - Method in class etomica.models.nitrogen.MeterBoltzmannDirect
getDataAsScalar() - Method in class etomica.models.nitrogen.MeterDirectInitPert
getDataAsScalar() - Method in class etomica.models.nitrogen.MeterOrientationOrderParameter
getDataAsScalar() - Method in class etomica.models.nitrogen.MeterRotPerturbMolecule
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAddDoubleSize
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtractDoubleSize
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterF
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterWidomMode
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
getDataAsScalar() - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityCO
getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityCO2
getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityO2
getDataAsScalar() - Method in class etomica.modules.chainequilibrium.MeterConversion
getDataAsScalar() - Method in class etomica.modules.colloid.MeterEnd2End
getDataAsScalar() - Method in class etomica.modules.dcvgcmd.MeterFlux
getDataAsScalar() - Method in class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
getDataAsScalar() - Method in class etomica.modules.entropylottery.MeterEntropy
getDataAsScalar() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterElongation
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterLoad
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterStrain
getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterStress
getDataAsScalar() - Method in class etomica.modules.mu.MeterDensitySides
getDataAsScalar() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
getDataAsScalar() - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
getDataAsScalar() - Method in class etomica.modules.osmosis.MeterOsmoticPressure
getDataAsScalar() - Method in class etomica.modules.pistoncylinder.DataSourceWallPressure
getDataAsScalar() - Method in class etomica.modules.rheology.MeterEndToEnd
getDataAsScalar() - Method in class etomica.modules.rheology.MeterNormalStress
getDataAsScalar() - Method in class etomica.modules.rheology.MeterViscosity
getDataAsScalar() - Method in class etomica.modules.sam.MeterWallPressure
getDataAsScalar() - Method in class etomica.modules.vle.MeterPressure2: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getDataAsScalar() - Method in class etomica.normalmode.DataSourceAvgPressure
getDataAsScalar() - Method in class etomica.normalmode.DataSourceAvgPressure2
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootPressure
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootPressure
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot1
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootPressure
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRootPMatch
getDataAsScalar() - Method in class etomica.normalmode.MeterAPIPotentialEnergy
getDataAsScalar() - Method in class etomica.normalmode.MeterDisplacementMoleculeRMS
getDataAsScalar() - Method in class etomica.normalmode.MeterDisplacementRMS
getDataAsScalar() - Method in class etomica.normalmode.MeterHarmonicCoordinate
getDataAsScalar() - Method in class etomica.normalmode.MeterHarmonicEnergy
getDataAsScalar() - Method in class etomica.normalmode.MeterHarmonicEnergyFromMove
getDataAsScalar() - Method in class etomica.normalmode.MeterJacobian
getDataAsScalar() - Method in class etomica.normalmode.MeterMaxExpansion
getDataAsScalar() - Method in class etomica.normalmode.MeterPhiDeviation
getDataAsScalar() - Method in class etomica.normalmode.MeterPressureSuperBox: Computes total pressure in box by summing virial over all pairs, and adding ideal-gas contribution.
getDataAsScalar() - Method in class etomica.normalmode.MeterThetaDeviation
getDataAsScalar() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
getDataAsScalar() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
getDataAsScalar() - Method in class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
getDataAsScalar() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
getDataAsScalar() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
getDataAsScalar() - Method in class etomica.spin.MeterSpin
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlockless: Returns null (any data is good data)
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim: Returns null (any data is good data)
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageCollapsing: Checks that incoming Data implements Data, and returns null if this is so.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageCollapsingLog: Checks that incoming Data implements Data, and returns null if this is so.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixed: Returns null (any data is good data)
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixedOutputFile: Returns null (any data is good data)
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorCounter: Returns null, indicating that any Data type is acceptable for input.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorHistogram: Returns null.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorHistory: Returns null.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataArrayWriter
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataDistributer
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataDump
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataFork: Returns null, indicating that this DataSink can accept any type of Data.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataGroupFilter: Returns null if the given DataInfo is for a DataGroup; otherwise throws an exception.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataGroupSplitter
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataHistogram: Returns caster that ensures accumulator will receive a DataDoubleArray.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataLogger
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorChemicalPotential
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorFunction: Always returns null.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorInterfacialTension
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataPump: Returns null, indicating that this DataSink can handle any type of Data without casting.
getDataCaster(IEtomicaDataInfo) - Method in interface etomica.data.DataSet.DataCasterJudge
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataSet.DataSetSink
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataSinkConsole: Returns null, indicating that any type of Data can be put here without casting.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataSinkTable.DataCasterJudgeTable
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataSplitter
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.DataTableWriter
getDataCaster(IEtomicaDataInfo) - Method in interface etomica.data.IDataSink: Returns a DataProcessor that casts the data that will be given to this DataSink to a form that it can accept.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.types.CastGroupOfTablesToDataTable: Returns null.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.types.CastGroupToDoubleArray: Returns null.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.types.CastToDouble: Returns null.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.types.CastToDoubleArray
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.types.CastToGroup: Returns null, indicating that this DataProcessor can accept any Data type.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.data.types.CastToTable: Returns null, indicating the this DataProcessor can handle (almost) any Data type.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.densityofstate.DataProcessorPhi
getDataCaster(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayPlot.DataCasterJudgeFunction
getDataCaster(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayTextBox: Returns caster needed to convert type indicated by DataInfo to a DataDouble.
getDataCaster(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayTextBoxesCAE
getDataCaster(IEtomicaDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweight
getDataCaster(IEtomicaDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
getDataCaster(IEtomicaDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
getDataCaster(IEtomicaDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
getDataCaster(IEtomicaDataInfo) - Method in class etomica.meam.DataProcessorCvMD
getDataCaster(IEtomicaDataInfo) - Method in class etomica.metastable.DataProcessorXY
getDataCaster(IEtomicaDataInfo) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.entropylottery.EntropyProcessor
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.FitTanh
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBias
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorVar
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
getDataCaster(IEtomicaDataInfo) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
getDataCaster(IEtomicaDataInfo) - Method in class etomica.normalmode.BoltzmannProcessor
getDataCaster(IEtomicaDataInfo) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
getDataCaster(IEtomicaDataInfo) - Method in class etomica.normalmode.DataProcessorSum
getDataCaster(IEtomicaDataInfo) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
getDataCaster(IEtomicaDataInfo) - Method in class etomica.surfacetension.FitTanh
getDataCaster(IEtomicaDataInfo) - Method in class etomica.surfacetension.SurfaceTensionMapped
getDataCaster(IEtomicaDataInfo) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
getDataCaster(IEtomicaDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
getDataCaster(IEtomicaDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
getDataCasterJudge() - Method in class etomica.data.DataSet
getDataCount() - Method in class etomica.data.DataSet
getDataDouble() - Method in class etomica.data.DataSourceScalar: Causes the single getDataAsScalar(Box) value to be computed and returned for the given box.
getDataFromSet(DataTag[]) - Method in class etomica.graphics.DisplayPlot
getDataHistogramBetaUAWf() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getDataHistogramBetaUAWf() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getDataHistogramBetaUAWr() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getDataHistogramBetaUAWr() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getDataHistogramBetaUBWf() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getDataHistogramBetaUBWf() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getDataHistogramBetaUBWr() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getDataHistogramBetaUBWr() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getDataImaginary(int, int) - Method in class etomica.lattice.LatticeSumCrystal.DataGroupLSC: Returns imaginary part of complex data.
getDataImaginary(int, int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular.DataGroupLSC: Returns imaginary part of complex data.
getDataImaginary(int, int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol.DataGroupLSCParacetamol: Returns imaginary part of complex data.
getDataInfo() - Method in class etomica.data.AccumulatorHistogram: Returns the DataInfo for the output Data.
getDataInfo() - Method in class etomica.data.AccumulatorHistory
getDataInfo() - Method in class etomica.data.DataDump
getDataInfo() - Method in class etomica.data.DataHistogram: Returns the DataInfo for the output Data.
getDataInfo() - Method in class etomica.data.DataProcessor
getDataInfo() - Method in class etomica.data.DataSet.DataSetSink
getDataInfo(int) - Method in class etomica.data.DataSet: Returns the ith DataInfo from the set.
getDataInfo() - Method in class etomica.data.DataSourceFunction
getDataInfo() - Method in class etomica.data.DataSourceGroup
getDataInfo() - Method in class etomica.data.DataSourcePoints
getDataInfo() - Method in class etomica.data.DataSourceRmsVelocity
getDataInfo() - Method in class etomica.data.DataSourceScalar
getDataInfo() - Method in class etomica.data.DataSourceTensorVirialHard
getDataInfo() - Method in class etomica.data.DataSourceUniform
getDataInfo() - Method in class etomica.data.HistogramDataSource: Returns the DataInfo for the output Data.
getDataInfo() - Method in interface etomica.data.IEtomicaDataSource
getDataInfo() - Method in class etomica.data.meter.MeterDihedralAngle
getDataInfo() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
getDataInfo() - Method in class etomica.data.meter.MeterHyperVirial
getDataInfo() - Method in class etomica.data.meter.MeterMomentumCOM
getDataInfo() - Method in class etomica.data.meter.MeterPositionCOM
getDataInfo() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
getDataInfo() - Method in class etomica.data.meter.MeterPressureByVolumeChange
getDataInfo() - Method in class etomica.data.meter.MeterPressureHardTensor
getDataInfo() - Method in class etomica.data.meter.MeterPressureTensor
getDataInfo() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
getDataInfo() - Method in class etomica.data.meter.MeterProfile
getDataInfo() - Method in class etomica.data.meter.MeterProfileByAtoms
getDataInfo() - Method in class etomica.data.meter.MeterProfileByVolume
getDataInfo() - Method in class etomica.data.meter.MeterRDF
getDataInfo() - Method in class etomica.data.meter.MeterRDFPC
getDataInfo() - Method in class etomica.data.meter.MeterTensorVelocity
getDataInfo() - Method in class etomica.freeenergy.npath.DataSourceEnergies
getDataInfo() - Method in class etomica.gaussianwork.MeterBoltzmannA
getDataInfo() - Method in class etomica.gaussianwork.MeterBoltzmannB
getDataInfo() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getDataInfo() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getDataInfo() - Method in class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
getDataInfo() - Method in class etomica.integrator.IntegratorPT.BoxTracker
getDataInfo() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
getDataInfo() - Method in class etomica.liquidLJ.MeterPU
getDataInfo() - Method in class etomica.liquidLJ.MeterPUCut
getDataInfo() - Method in class etomica.liquidLJ.MeterPUCutLS
getDataInfo() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
getDataInfo() - Method in class etomica.mappedvirial.MeterMeanForce
getDataInfo() - Method in class etomica.metastable.MeterDensityDistribution
getDataInfo() - Method in class etomica.models.nitrogen.MeterBoltzmann
getDataInfo() - Method in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
getDataInfo() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
getDataInfo() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
getDataInfo() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
getDataInfo() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
getDataInfo() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getDataInfo() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getDataInfo() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
getDataInfo() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
getDataInfo() - Method in class etomica.models.oneDHardRods.MeterOverlap
getDataInfo() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
getDataInfo() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
getDataInfo() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
getDataInfo() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
getDataInfo() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getDataInfo() - Method in class etomica.modules.droplet.MeterDeformation
getDataInfo() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
getDataInfo() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
getDataInfo() - Method in class etomica.modules.mu.DataSourceWallPressureMu
getDataInfo() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getDataInfo() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getDataInfo() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
getDataInfo() - Method in class etomica.modules.rosmosis.MeterFlux
getDataInfo() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
getDataInfo() - Method in class etomica.modules.sam.MeterTilt
getDataInfo() - Method in class etomica.normalmode.DataSourceFE
getDataInfo() - Method in class etomica.normalmode.DataSourceFEHistogram
getDataInfo() - Method in class etomica.normalmode.DataSourceImposedFEFit
getDataInfo() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getDataInfo() - Method in class etomica.normalmode.DataSourcePMu
getDataInfo() - Method in class etomica.normalmode.DataSourcePN
getDataInfo() - Method in class etomica.normalmode.MeterAtomicDisplacement
getDataInfo() - Method in class etomica.normalmode.MeterBoltzmann
getDataInfo() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
getDataInfo() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getDataInfo() - Method in class etomica.normalmode.MeterBoltzmannTarget
getDataInfo() - Method in class etomica.normalmode.MeterDADB
getDataInfo() - Method in class etomica.normalmode.MeterDDP
getDataInfo() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
getDataInfo() - Method in class etomica.normalmode.MeterDirectSamplingTarget
getDataInfo() - Method in class etomica.normalmode.MeterDP
getDataInfo() - Method in class etomica.normalmode.MeterHarmonicCoordinate
getDataInfo() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
getDataInfo() - Method in class etomica.normalmode.MeterNormalMode
getDataInfo() - Method in class etomica.normalmode.MeterOverlapSwitch
getDataInfo() - Method in class etomica.normalmode.MeterPlaneSlip
getDataInfo() - Method in class etomica.normalmode.MeterSamplingHarmonic
getDataInfo() - Method in class etomica.normalmode.MeterSamplingTarget
getDataInfo() - Method in class etomica.normalmode.MeterSolidDA
getDataInfo() - Method in class etomica.normalmode.MeterSolidDACut
getDataInfo() - Method in class etomica.normalmode.MeterSolidMirror
getDataInfo() - Method in class etomica.normalmode.MeterSolidProps
getDataInfo() - Method in class etomica.normalmode.MeterSolidPropsLJ
getDataInfo() - Method in class etomica.normalmode.MeterTargetTP
getDataInfo() - Method in class etomica.normalmode.MeterTilt
getDataInfo() - Method in class etomica.normalmode.MeterTiltHistogram
getDataInfo() - Method in class etomica.normalmode.MeterTiltRotation
getDataInfo() - Method in class etomica.normalmode.MeterTiltRotationHistogram
getDataInfo() - Method in class etomica.normalmode.MeterTiltRotationStdev
getDataInfo() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
getDataInfo() - Method in class etomica.normalmode.MeterWorkBennetTarget
getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetBennet
getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
getDataInfo() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
getDataInfo() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
getDataInfo() - Method in class etomica.overlap.MeterOverlap
getDataInfo() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
getDataInfo() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
getDataInfo() - Method in interface etomica.util.FunctionGeneral: Returns a DataInfo that describes the Data object that is returned by this function's f method.
getDataInfo() - Method in class etomica.virial.MeterSamplingWeight
getDataInfo() - Method in class etomica.virial.MeterVirial
getDataInfo() - Method in class etomica.virial.MeterVirialBD
getDataInfo() - Method in class etomica.virial.MeterVirialBDBin
getDataInfo() - Method in class etomica.virial.MeterVirialExternalField
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldConfined
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldRho
getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldSW
getDataInfo() - Method in class etomica.virial.MeterVirialIC
getDataInfo() - Method in class etomica.virial.MeterVirialSWWE
getDataInfoHistogramBetaUAWf() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getDataInfoHistogramBetaUAWf() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getDataInfoHistogramBetaUAWr() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getDataInfoHistogramBetaUAWr() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getDataInfoHistogramBetaUBWf() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getDataInfoHistogramBetaUBWf() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getDataInfoHistogramBetaUBWr() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getDataInfoHistogramBetaUBWr() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getDataLength() - Method in class etomica.integrator.IntegratorPT.BoxTracker
getDataOverlap() - Method in class etomica.normalmode.SimOverlapModule
getDataPumps() - Method in class etomica.thermointegration.IntegratorThermodynamic
getDataReal(int, int) - Method in class etomica.lattice.LatticeSumCrystal.DataGroupLSC: Returns real part of complex data.
getDataReal(int, int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular.DataGroupLSC: Returns real part of complex data.
getDataReal(int, int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol.DataGroupLSCParacetamol: Returns real part of complex data.
getDataResetAction() - Method in class etomica.action.SimulationRestart
getDataReweighted() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
getDataReweighted() - Method in class etomica.normalmode.MeterWorkTargetBennet
getDataReweighted() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
getDataReweighted() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
getDataSet() - Method in class etomica.graphics.DisplayPlot: Returns the DataSinkTable instance that specifies the plot data.
getDataSink(int) - Method in class etomica.data.DataDistributer: Returns the DataSink for the ith output stream (corresponding to the ith numerical value coming in).
getDataSink(int) - Method in class etomica.data.DataGroupSplitter: Returns the DataSink for the ith output stream (corresponding to the ith numerical value coming in).
getDataSink() - Method in class etomica.data.DataProcessor
getDataSink() - Method in class etomica.data.DataProcessorForked
getDataSink(int) - Method in class etomica.data.DataSplitter: Returns the DataSink for the ith output stream (corresponding to the ith numerical value coming in).
getDataSink(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getDataSink(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
getDataSinks() - Method in class etomica.data.DataFork
getDataSinks() - Method in interface etomica.data.DataPipeForked
getDataSinks() - Method in class etomica.data.DataProcessorForked
getDataSource() - Method in class etomica.data.DataPump
getDataSource() - Method in class etomica.data.meter.MeterProfile: The meter that defines the profiled quantity
getDataSource() - Method in class etomica.data.meter.MeterProfileByAtoms: The meter that defines the profiled quantity
getDataSource() - Method in class etomica.data.meter.MeterProfileByVolume: The meter that defines the profiled quantity
getDataSource() - Method in class etomica.simulation.DataStreamHeader
getDataStreamPumps() - Method in class etomica.action.SimulationDataAction
getDataStreamPumps() - Method in class etomica.graphics.DeviceTrioControllerButton: Returns an ArrayList of DataPumps that are headers for the data streams.
getDataTable() - Method in class etomica.graphics.DisplayTable
getDataTagBag(LinkedList<DataTagBag>, DataTag[]) - Static method in class etomica.graphics.DataTagBag: Returns the first DataTagBag from the given list that has no non-matching tags with the given desiredTags
getDataTagBagExact(LinkedList<DataTagBag>, DataTag[]) - Static method in class etomica.graphics.DataTagBag: Return the DataTagBag with the given set of tags (exactly) if it exists, or null of no such DataTagBag exists.
getDateFormat() - Method in interface org.jmol.api.ApiPlatform
getDateFormat() - Method in class org.jmol.awt.Platform
getDBOType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
getDecimalSliderMajorTickSpacing() - Method in class etomica.graphics.DecimalSlider
getDecimalSliderMaximum() - Method in class etomica.graphics.DecimalSlider
getDecimalSliderMinimum() - Method in class etomica.graphics.DecimalSlider
getDecimalSliderMinorTickSpacing() - Method in class etomica.graphics.DecimalSlider
getDecimalSliderValue() - Method in class etomica.graphics.DecimalSlider
getDefaultColor() - Method in class etomica.graphics.ColorScheme
getDefaultFontFamily() - Method in class etomica.graph.view.rasterizer.SVGConverter
getDeformation() - Method in class etomica.modules.droplet.ConfigurationDroplet
getDegeneracy() - Method in class etomica.math.discrete.PermutationDegenerateIterator
getDelayExponent() - Method in class etomica.graphics.DeviceDelaySlider
getDeltaCut() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizable
getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
getDeltaN() - Method in class etomica.modules.dcvgcmd.MyMCMove
getDeltaU(IAtomKinetic, double, boolean, boolean) - Method in class etomica.modules.mu.P1MagicWall
getDeltaU(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
getDeltaX() - Method in class etomica.util.HistogramExpanding
getDenominator() - Method in interface etomica.graph.model.Coefficient
getDenominator() - Method in class etomica.graph.model.impl.CoefficientImpl
getDenstiyProfileDump() - Method in class etomica.data.DataProcessorChemicalPotential
getDepth() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Get depth percentage
getDepth() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Get depth percentage
getDepth() - Method in class org.jmol.util.GData: gets g3d depth
getDepthPercent() - Method in class g3dsys.control.G3DSys
getDescent() - Method in class org.jmol.util.JmolFont
getDescription(String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getDescription() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getDescription() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getDestination() - Method in class etomica.action.MoleculeActionTranslateTo
getDestinationFile(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Get the name of the result image file.
getDestinationType() - Method in class etomica.graph.view.rasterizer.SVGConverter
getDeviationVector() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
getdFdr(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
getdFdr(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
getdfdT(int, double, double) - Static method in class etomica.virial.B3LJ: Returns a discretized df/dT function containing N points with a separation interval of del_r
getDiagonalElements() - Method in class etomica.math.linearalgebra.EigenSystemReduction
getDiameter(IAtom) - Method in interface etomica.atom.DiameterHash: Returns an appropriate diameter for the given atom.
getDiameter(IAtom) - Method in class etomica.atom.DiameterHashByElement
getDiameter(IElement) - Method in class etomica.atom.DiameterHashByElement
getDiameter(IAtom) - Method in class etomica.atom.DiameterHashByElementType
getDiameter(IAtom) - Method in class etomica.atom.DiameterHashByType
getDiameter(IAtomType) - Method in class etomica.atom.DiameterHashByType
getDiameterHash() - Method in class etomica.graphics.DisplayBox: Returns the DiameterHash used by this DisplayBox.
getDiameterHashByElement() - Method in class etomica.atom.DiameterHashByElementType
getDielectric() - Method in class etomica.potential.P2ReactionFieldDipole: Returns the dielectric constant of the fluid surrounding the cavity.
getDielectric() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated: Returns the dielectric constant of the fluid surrounding the cavity.
getDiffusePercent() - Static method in class org.jmol.util.GData
getDim() - Method in class etomica.modules.rosmosis.MeterFlux
getDimension() - Method in class etomica.conjugategradient.DerivativeEnergyFunction
getDimension() - Method in class etomica.conjugategradient.TestFiniteDifferenceDerivative
getDimension() - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
getDimension() - Method in class etomica.data.DataInfo
getDimension() - Method in class etomica.data.DataInfoFactory: Returns the dimension
getDimension() - Method in interface etomica.data.IEtomicaDataInfo
getDimension() - Method in interface etomica.data.IEtomicaDataInfoFactory: Returns the dimension
getDimension() - Method in class etomica.data.meter.MeterTemperature
getDimension() - Method in class etomica.graphics.Device
getDimension() - Method in interface etomica.modifier.Modifier: Returns the dimension of the property being modified.
getDimension() - Method in class etomica.modifier.ModifierGeneral
getDimension() - Method in class etomica.modifier.ModifierNMolecule
getDimension() - Method in class etomica.modifier.ModifyAction
getDimension() - Method in class etomica.modules.adsorption.ModifierPMu
getDimension(double, double) - Method in class etomica.modules.clustergenerator.Plot: Computes the separation in pixels of two points in the world window.
getDimension() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
getDimension() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
getDimension() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
getDimension() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
getDimension() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
getDimension() - Method in class etomica.modules.entropylottery.ModifierDimensions
getDimension() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
getDimension() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
getDimension() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
getDimension() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
getDimension() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
getDimension() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
getDimension() - Method in class etomica.normalmode.ModifierCells3D
getDimension() - Method in class etomica.normalmode.ModifierXCells2D
getDimension() - Method in class etomica.normalmode.ModifierYCells2D
getDimension() - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
getDimension() - Method in interface etomica.units.Dimensioned
getDimension() - Method in interface etomica.util.FunctionMultiDimensional: The dimension of the space of independent variables.
getDimension() - Method in class etomica.util.numerical.CalcGradientDifferentiable
getDimension() - Method in class etomica.util.numerical.FiniteDifferenceDerivative
getDimension() - Method in class etomica.virial.simulations.ModifierTPI
getDimensions() - Method in class etomica.lattice.CellLattice: Returns the array that specifies the spatial dimensions of the lattice of cells.
getDimerAtomType() - Method in class etomica.normalmode.SpeciesHSDimer
getDimx() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
getDimy() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
getDipole(IMolecule) - Method in class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
getDipole(IMolecule) - Method in class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
getDipole(IMolecule) - Method in interface etomica.atom.DipoleSource: Returns the dipole of the given molecule.
getDipole(IMolecule) - Method in class etomica.dielectric.DHS_NVT.DipoleSourceDHS
getDipole(IMolecule) - Method in class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
getDipole(IMolecule) - Method in class etomica.dielectric.TIP4P_NVT.DipoleSourceTIP4PWater
getDipole(IMolecule) - Method in class etomica.models.aceticAcid.DipoleSourceAceticAcid
getDipole(IMolecule) - Method in class etomica.models.water.DipoleSourceWater
getDipole1() - Method in class etomica.models.water.P2WaterTIP4PHardCore
getDipole2() - Method in class etomica.models.water.P2WaterTIP4PHardCore
getDipoleMomentSquare() - Method in class etomica.rotation.P2LJDipole
getDipoleSource() - Method in class etomica.potential.P2ReactionFieldDipole: Returns the dipole source used by this object.
getDipoleSource() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated: Returns the dipole source used by this object.
getDipoleStrength() - Method in class etomica.models.water.DipoleSourceWater: Returns the dipole strength.
getDirectedNormalThroughPoints(Point3f, Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
getDirection() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Gets the direction (up or down list) of the neighbors given by the iterator.
getDirection() - Method in interface etomica.space.IOrientation: Returns a unit vector pointing in the orientation's direction.
getDirection() - Method in class etomica.space2d.Orientation2D
getDirection() - Method in class etomica.space3d.Orientation3D
getDirection() - Method in class etomica.space3d.OrientationFull3D
getDirection() - Method in class etomica.spin.P1MagneticField
getDiscardProperty() - Method in class etomica.graph.operations.SplitParameters
getDisplayBox(IBox) - Method in class etomica.graphics.SimulationGraphic
getDisplayDensity() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
getDisplayDensity() - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
getDisplayDensity() - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
getDisplayPlot() - Method in class etomica.graphics.DevicePlotPoints: Returns the top level panel that the function plot components sit on.
getDistanceToOrigin() - Method in class etomica.math.geometry.Plane: Perpendicular distance from the plane to the origin.
getDitheredNoisyShadeIndex(float, float, float, float) - Static method in class org.jmol.util.Shader
getDoApplyPBC() - Method in class etomica.action.WriteConfiguration: Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() - Method in class etomica.action.WriteConfigurationBinary: Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() - Method in class etomica.action.WriteConfigurationDLPOLY: Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() - Method in class etomica.action.WriteConfigurationP2DLPOLY: Returns true if PBC are applied to coordinates written to the file.
getDoApplyPBC() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
getDoApplyPBC() - Method in class etomica.nbr.cell.NeighborCellManager
getDoApplyPBC() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getDoApplyPBC() - Method in class etomica.nbr.list.NeighborListManager
getDoAveraging() - Method in class etomica.util.HistogramNotSoSimple
getDoCov() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
getDoEnforceBounds() - Method in class etomica.data.DataSourceUniform
getDoExcludeNonNeighbors() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert: Returns true if the move does not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
getDoExcludeNonNeighbors() - Method in class etomica.normalmode.MCMoveAtomCoupled: Returns true if the move does not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
getDoExcludeNonNeighbors() - Method in class etomica.normalmode.MCMoveMoleculeCoupled: Returns true if the move does not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
getDoIncludeACInError() - Method in class etomica.data.AccumulatorAverage
getDoShowCurrent() - Method in class etomica.graphics.DisplayTextBoxesCAE
getDoStrictBlockData() - Method in class etomica.data.AccumulatorAverageFixed
getDoubleArray() - Method in class etomica.math.Quaternion: Returns the Quaternion as a double array
getDoubleAvg() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
getDoubleDefaultParameters(String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getDoubleVar() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
getDoWiggle() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
getDownList() - Method in class etomica.nbr.list.AtomNeighborLists: Returns an array of downlist-neighbor-atom lists.
getDownList() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists: Returns an array of downlist-neighbor-molecule lists.
getDownList(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getDownList(IAtom) - Method in class etomica.nbr.list.NeighborListManager
getDrawables() - Method in class etomica.graphics.DisplayBox
getDrawBoundary() - Method in class etomica.graphics.DisplayCanvas
getDrawBoundaryType() - Method in class g3dsys.images.ImageShell: Gets the boundary drawing style
getDrawingHeight() - Method in class etomica.graphics.DisplayBox: return int : height of the drawing area (only relevant for 1D)
getDrawOverflow() - Method in class etomica.graphics.DisplayBox
getDrawSize() - Method in class etomica.graphics.DisplayBox
getDrawSize() - Method in class etomica.graphics.DisplayPolytope
getDst() - Method in class etomica.graph.view.rasterizer.SVGConverter
getDv() - Method in class etomica.modules.droplet.P2Cohesion
getDy12(int) - Method in class etomica.util.numerical.AkimaSplineSmoother
getE1() - Method in class etomica.graph.isomorphism.AbstractSearchState
getE1(byte, byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
getE2() - Method in class etomica.graph.isomorphism.AbstractSearchState
getE2(byte, byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
getE2CliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
getE2Cliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
getECliqueCount() - Method in class etomica.virial.ClusterSumHS
getECliqueCount() - Method in interface etomica.virial.ClusterWheatley: Returns number of e-bond cliques for the configuration passed to checkConfig
getECliqueCount() - Method in class etomica.virial.ClusterWheatleyHS
getECliqueCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getECliques() - Method in class etomica.virial.ClusterSumHS
getECliques() - Method in interface etomica.virial.ClusterWheatley: Returns an array containing the clique sets (based on e-bonds) for the configuration passed to checkConfig.
getECliques() - Method in class etomica.virial.ClusterWheatleyHS
getECliques() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getEdge(byte) - Method in interface etomica.graph.model.Graph
getEdge(byte, byte) - Method in interface etomica.graph.model.Graph
getEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
getEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
getEdgeCount() - Method in class etomica.virial.ClusterSumHS: Returns edgeCount (number of overlaps) of configuration passed to checkConfig
getEdgeCount() - Method in interface etomica.virial.ClusterWheatley: Returns edgeCount (number of overlaps) of configuration passed to checkConfig
getEdgeCount() - Method in class etomica.virial.ClusterWheatleyHS: Returns edgeCount (number of overlaps) of configuration passed to checkConfig
getEdgeCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening: Returns edgeCount (number of overlaps) of configuration passed to checkConfig
getEdgeId(byte, byte) - Method in interface etomica.graph.model.Graph
getEdgeId(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
getEdgeLength() - Method in class etomica.math.geometry.Cube
getEdgeLength() - Method in class etomica.math.geometry.Square
getEdgeLength() - Method in class etomica.math.geometry.TruncatedOctahedron
getEdgeLengths() - Method in class etomica.math.geometry.Cuboid: Returns a vector with elements equal to the edge lengths of the cuboid.
getEdgeLengths() - Method in class etomica.math.geometry.LineSegment: Returns the length of the line segment as the element of a 1D vector.
getEdgeLengths() - Method in class etomica.math.geometry.Rectangle: Returns a vector with elements equal to the edge lengths of the rectangle.
getEdgeLengths() - Method in interface etomica.math.geometry.Rectangular
getEdges() - Method in class etomica.math.geometry.LineSegment
getEdges() - Method in class etomica.math.geometry.Point
getEdges() - Method in class etomica.math.geometry.Polygon: Returns all edges defined by the polygon.
getEdges() - Method in class etomica.math.geometry.Polyhedron: Returns all edges defined by the polyhedron.
getEdges() - Method in class etomica.math.geometry.Polytope
getEdgeVector(int) - Method in interface etomica.api.IBoundary: Returns the vector that defines the edge of this boundary for the given dimension.
getEdgeVector(int) - Method in class etomica.space.BoundaryDeformablePeriodic
getEdgeVector(int) - Method in class etomica.space.BoundaryRectangular
getEdgeVector(int) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
getEditValues() - Method in class etomica.graphics.DeviceSlider
getEditVariables() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getEditVariables() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getEFCliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
getEFCliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
getEigenValue(int) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
getEigenvalues() - Method in class org.jmol.util.Eigen
getEigenVectorElement(int, int) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
getEigenVectors() - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
getEigenvectors() - Method in interface etomica.normalmode.NormalModes: First index corresponds to the wave vector; second index gives the eigenvector, and third index gives the elements of the vector.
getEigenvectors() - Method in class etomica.normalmode.NormalModes1DHR
getEigenvectors() - Method in class etomica.normalmode.NormalModes2D
getEigenvectors() - Method in class etomica.normalmode.NormalModes3D
getEigenvectors() - Method in class etomica.normalmode.NormalModesFromFile
getEigenvectors() - Method in class etomica.normalmode.NormalModesMolecular
getEigenvectors() - Method in class etomica.normalmode.NormalModesPotential
getEigenvectors() - Method in class etomica.normalmode.NormalModesSoftSpherical
getEigenVectors() - Method in class etomica.normalmode.NormalModesVariable
getEigenvectors() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getEigenVectors3() - Method in class org.jmol.util.Eigen
getEigenvectorsFloatTransposed() - Method in class org.jmol.util.Eigen: transpose V and turn into floats
getElectrostatic() - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
getElement() - Method in interface etomica.api.IAtomType
getElement() - Method in class etomica.atom.AtomTypeLeaf
getElement() - Method in class etomica.chem.models.ModelChain: Returns the Element used for the leaf atoms in the chain, or null if no Element has been set (an ElementSimple will be used).
getElement(int, int) - Method in class org.jmol.util.Matrix3f: Retrieves the value at the specified row and column of this matrix.
getElement(int, int) - Method in class org.jmol.util.Matrix4f: Retrieves the value at the specified row and column of this matrix.
getElementHash() - Method in class etomica.action.WriteConfigurationDLPOLY
getElementHash() - Method in class etomica.action.WriteConfigurationP2DLPOLY
getElementNumber(short) - Static method in class org.jmol.util.Elements
getEllipsoid(Vector3f[], float[], boolean) - Static method in class org.jmol.util.Eigen
getEllipsoidDD(double[][]) - Static method in class org.jmol.util.Eigen
getEllipsoidShade(float, float, float, int, Matrix4f) - Static method in class org.jmol.util.Shader
getEmbeddedSpace() - Method in class etomica.math.geometry.Polytope: The space defining the vectors used to represent the vertices.
getEnabled() - Method in class etomica.util.Grabber.DefaultMouseListener
getEnd() - Method in class g3dsys.images.Line
getEndpoint1() - Method in class g3dsys.images.Bond
getEndpoint2() - Method in class g3dsys.images.Bond
getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
getEnergy(IVectorMutable[], IVectorMutable[]) - Method in class etomica.potential.P2WaterPotentialsJankowski
getEnergySum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
getEnergySum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
getEntries() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
getEpsilon() - Method in class etomica.models.water.P2Water3P
getEpsilon() - Method in class etomica.models.water.P2Water3PSoft
getEpsilon() - Method in class etomica.models.water.P2Water4P
getEpsilon() - Method in class etomica.models.water.P2Water4PSoft
getEpsilon() - Method in class etomica.models.water.P2WaterTIP4P
getEpsilon() - Method in class etomica.models.water.P2WaterTIP4PHardCore
getEpsilon() - Method in class etomica.modules.adsorption.P1Wall
getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellBonding: Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellSurface: Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.colloid.P1Wall
getEpsilon() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
getEpsilon() - Method in class etomica.modules.dcvgcmd.P1WCAWall
getEpsilon() - Method in class etomica.modules.droplet.P2Cohesion
getEpsilon() - Method in class etomica.modules.mu.P2SquareWellOneSide: Accessor method for depth of well
getEpsilon() - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
getEpsilon() - Method in class etomica.modules.rosmosis.P1Tether
getEpsilon() - Method in class etomica.modules.sam.P1WCAWall
getEpsilon() - Method in class etomica.modules.vle.VLESim
getEpsilon() - Method in class etomica.potential.P22CLJQ
getEpsilon() - Method in class etomica.potential.P2Exp6Buckingham
getEpsilon() - Method in class etomica.potential.P2HardAssociation: Accessor method for depth of well.
getEpsilon() - Method in class etomica.potential.P2HardAssociationCone: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2LennardJones: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2LennardJonesDreiding: Accessor method for Lennard-Jones energy parameter
getEpsilon() - Method in class etomica.potential.P2LJDipole
getEpsilon() - Method in class etomica.potential.P2LJQ
getEpsilon() - Method in class etomica.potential.P2LJQQ
getEpsilon() - Method in class etomica.potential.P2ModifiedMorse
getEpsilon() - Method in class etomica.potential.P2Morse
getEpsilon() - Method in class etomica.potential.P2PenetrableSphere: Mutator method for height of core.
getEpsilon() - Method in class etomica.potential.P2PenetrableSquareWell: Accessor method for depth of well
getEpsilon() - Method in class etomica.potential.P2SoftSphere: Accessor method for soft-sphere energy parameter
getEpsilon() - Method in class etomica.potential.P2SquareWell: Accessor method for depth of well
getEpsilon() - Method in class etomica.potential.P2SquareWellRobust: Accessor method for depth of well
getEpsilon() - Method in class etomica.potential.P2TriangleWell
getEpsilon() - Method in class etomica.potential.P2WCA: Accessor method for the energy parameter
getEpsilon() - Method in class etomica.potential.P3BondAngle: Returns the characteristic energy of the potential
getEpsilon() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig: Returns the characteristic energy of the potential
getEpsilon() - Method in class etomica.rotation.P2LJDipole
getEpsilon() - Method in class etomica.units.systems.LJ
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getEpsilon() - Method in class etomica.yukawa.P2HC2Yukawa
getEpsilon6() - Method in class etomica.potential.P2Exp6Buckingham
getEpsilonBonding() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getEpsilonBonding() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getEpsilonC() - Method in class etomica.potential.P2CO2EMP
getEpsilonCG() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
getEpsilonCO() - Method in class etomica.potential.P2CO2EMP
getEpsilonCore() - Method in class etomica.potential.P2DoubleWell: Accessor method for depth of well
getEpsilonCore() - Method in class etomica.potential.P2PenetrableSquareWell
getEpsilonCoreDimension() - Method in class etomica.potential.P2PenetrableSquareWell
getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
getEpsilonDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
getEpsilonDimension() - Method in class etomica.potential.P2DoubleWell
getEpsilonDimension() - Method in class etomica.potential.P2HardAssociation
getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationCone
getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
getEpsilonDimension() - Method in class etomica.potential.P2LennardJones
getEpsilonDimension() - Method in class etomica.potential.P2LennardJonesDreiding
getEpsilonDimension() - Method in class etomica.potential.P2ModifiedMorse
getEpsilonDimension() - Method in class etomica.potential.P2Morse
getEpsilonDimension() - Method in class etomica.potential.P2PenetrableSphere
getEpsilonDimension() - Method in class etomica.potential.P2PenetrableSquareWell
getEpsilonDimension() - Method in class etomica.potential.P2SoftSphere
getEpsilonDimension() - Method in class etomica.potential.P2SquareWell
getEpsilonDimension() - Method in class etomica.potential.P2SquareWellRobust
getEpsilonDimension() - Method in class etomica.potential.P2TriangleWell
getEpsilonDimension() - Method in class etomica.potential.P2WCA
getEpsilonDimension() - Method in class etomica.potential.P3BondAngle
getEpsilonDimension() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
getEpsilonNR() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
getEpsilonO() - Method in class etomica.potential.P2CO2EMP
getEpsilonWell() - Method in class etomica.potential.P2DoubleWell
getEpsInner() - Method in class etomica.potential.P2PenetrableBond
getEpsInnerDimension() - Method in class etomica.potential.P2PenetrableBond
getEpsOuter() - Method in class etomica.potential.P2PenetrableBond
getEpsOuterDimension() - Method in class etomica.potential.P2PenetrableBond
getEquationForQuadricWithCenter(float, float, float, Matrix3f, Vector3f, Matrix3f, double[], Matrix4f) - Static method in class org.jmol.util.Quadric
getError(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapAvg
getError(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getError(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
getError(int) - Method in class etomica.overlap.DataOverlap: Returns the error in the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the given value of the Bennet parameter.
getError() - Method in class etomica.virial.overlap.DataSourceVirialOverlap: Returns the error in the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the optimal value of the Bennet parameter.
getError(int) - Method in class etomica.virial.overlap.DataSourceVirialOverlap: Returns the error in the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the given value of the Bennet parameter.
getErrorCode() - Method in exception etomica.graph.view.rasterizer.SVGConverterException
getEta(int) - Method in class etomica.virial.cluster.ClusterOperations: Returns all diagrams of order n in the expansion for the indirect correlation function eta(r) = h(r) - c(r), in the presence of any approximations currently in effect.
getEValNum() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
getEValNum() - Method in class etomica.normalmode.IntegratorHarmonic
getEventInterval() - Method in class etomica.integrator.Integrator
getEventManager() - Method in class etomica.action.activity.Controller
getEventManager() - Method in interface etomica.action.activity.IController: Returns the event manager used by the controller to notify listeners of individual actions events as well as events related to the controller itself.
getEventManager() - Method in interface etomica.api.IBoundary
getEventManager() - Method in interface etomica.api.IBox: Returns the event manager for this box.
getEventManager() - Method in interface etomica.api.IIntegrator
getEventManager() - Method in interface etomica.api.ISimulation: Returns the Simulation's event manager, which fires events for Boxes and Species being added and removed.
getEventManager() - Method in class etomica.box.Box
getEventManager() - Method in class etomica.integrator.Integrator
getEventManager() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getEventManager() - Method in class etomica.nbr.list.NeighborListManager
getEventManager() - Method in class etomica.simulation.Simulation
getEventManager() - Method in class etomica.space.Boundary
getException(IAction) - Method in class etomica.action.activity.Controller: Returns the exception thrown by an action held by the controller.
getException(IAction) - Method in interface etomica.action.activity.IController: Returns the exception thrown by an action held by the controller.
getExecuteOnload() - Method in class etomica.graph.view.rasterizer.SVGConverter: Returns true if the scripts attached to the DOM using 'onload' event attribute is going to be executed before rasterizing, false otherwise.
getExp() - Method in class etomica.virial.MayerSSSeries: Returns the HS diameter.
getExpGroupingSize() - Method in class etomica.util.ScientificFormat
getExpMaximumIntegerDigits() - Method in class etomica.util.ScientificFormat
getExpMinimumIntegerDigits() - Method in class etomica.util.ScientificFormat
getExpNegativePrefix() - Method in class etomica.util.ScientificFormat
getExpNegativeSuffix() - Method in class etomica.util.ScientificFormat
getExponent() - Method in class etomica.potential.P2SoftSphere: Accessor method for soft-sphere softness parameter
getExportName() - Method in class org.jmol.g3d.Graphics3D
getExportType() - Method in class org.jmol.g3d.Graphics3D
getExpPositivePrefix() - Method in class etomica.util.ScientificFormat
getExpPositiveSuffix() - Method in class etomica.util.ScientificFormat
getExpression() - Method in class etomica.graph.engine.impl.AssignmentImpl
getExpression() - Method in class etomica.graph.engine.impl.UnaryOpImpl
getExpression() - Method in interface etomica.graph.engine.Parser.Assignment
getExpression() - Method in interface etomica.graph.engine.Parser.UnaryOp
getExpression1() - Method in class etomica.graph.engine.impl.BinaryOpImpl
getExpression1() - Method in interface etomica.graph.engine.Parser.BinaryOp
getExpression2() - Method in class etomica.graph.engine.impl.BinaryOpImpl
getExpression2() - Method in interface etomica.graph.engine.Parser.BinaryOp
getExtension() - Method in class etomica.graph.view.rasterizer.DestinationType
getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.VirialDiagrams
getExtraDisconnectedVirialGraphs(int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
getExtraDisconnectedVirialGraphs(int) - Method in class etomica.virial.cluster.VirialDiagramsPT
getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
getExtrapolatedLogError(int, int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getExtraTargetClusters() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
getF(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
getF(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
getF1CliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
getF1Cliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
getFaces() - Method in class etomica.math.geometry.Polyhedron: Returns all faces defined by the polyhedron.
getFaces() - Method in class org.jmol.util.MeshSurface
getFacesFromCriticalPoints(Point3f[]) - Static method in class org.jmol.util.BoxInfo
getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
getFactory() - Method in interface etomica.data.IEtomicaDataInfo: Returns a mutable factory that can make copies of this instance of DataInfo.
getFactory() - Method in class etomica.data.types.DataDouble.DataInfoDouble
getFactory() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
getFactory() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
getFactory() - Method in class etomica.data.types.DataFunction.DataInfoFunction
getFactory() - Method in class etomica.data.types.DataGroup.DataInfoGroup
getFactory() - Method in class etomica.data.types.DataTable.DataInfoTable
getFactory() - Method in class etomica.data.types.DataTensor.DataInfoTensor
getFactory() - Method in class etomica.data.types.DataVector.DataInfoVector
getFactory() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
getFalseLabel() - Method in class etomica.action.ActionToggle
getFalseLabel() - Method in class etomica.graphics.DeviceToggleButton
getFalseLabel() - Method in class etomica.graphics.DeviceToggleRadioButtons
getFieldColorMap() - Method in class etomica.graph.engine.impl.ConstructorColoredImpl
getFieldColorMap() - Method in interface etomica.graph.engine.Parser.ConstructorColored
getFieldNodes() - Method in class etomica.graph.engine.impl.ConstructorMonoImpl
getFieldNodes() - Method in interface etomica.graph.engine.Parser.ConstructorMono
getFigs() - Method in class g3dsys.control.G3DSys: For use only by ImageShell class for iteration
getFile() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
getFileName() - Method in class etomica.data.DataLogger
getFileName() - Method in class etomica.normalmode.NormalModesMolecular
getFileName() - Method in class etomica.normalmode.NormalModesPotential
getFileNRef(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
getFilter() - Method in class etomica.modules.droplet.MeterDeformation
getFirstVector() - Method in class etomica.config.ConformationChainZigZag
getFirstVector() - Method in class etomica.config.ConformationChainZigZag2
getFixedCOM() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
getFixedDeltaU() - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
getFixedDeltaU() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
getFixedDeltaU() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
getFixedDeltaU() - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
getFixedSpecies() - Method in class etomica.config.GrainBoundaryTiltConfiguration
getFluctuationFactor() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
getFM() - Method in class g3dsys.control.G3DSys: Only to be used internally to escape endless delegation
getFNonAdditiveValues() - Method in class etomica.virial.ClusterSumMultibody
getFont3D(float) - Method in class org.jmol.util.GData
getFont3D(byte) - Static method in class org.jmol.util.JmolFont
getFont3DCurrent() - Method in class org.jmol.g3d.Graphics3D
getFont3DCurrent() - Method in class org.jmol.util.GData
getFont3DFS(String, float) - Method in class org.jmol.util.GData
getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
getFont3DScaled(JmolFont, float) - Method in class org.jmol.util.GData
getFontAscent(Object) - Method in interface org.jmol.api.ApiPlatform
getFontAscent(Object) - Method in class org.jmol.awt.Platform
getFontDescent(Object) - Method in interface org.jmol.api.ApiPlatform
getFontDescent(Object) - Method in class org.jmol.awt.Platform
getFontFaceID(String) - Static method in class org.jmol.util.JmolFont
getFontFid(float) - Method in class org.jmol.util.GData
getFontFidFS(String, float) - Method in class org.jmol.util.GData
getFontMetrics(JmolFont, Object) - Method in interface org.jmol.api.ApiPlatform
getFontMetrics(JmolFont, Object) - Method in class org.jmol.awt.Platform
getFontStyleID(String) - Static method in class org.jmol.util.GData
getFontStyleID(String) - Static method in class org.jmol.util.JmolFont
getForce() - Method in class etomica.potential.P1HardMovingBoundary
getForceconstant() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getForceconstant() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getForceDimension() - Method in class etomica.potential.P1HardMovingBoundary
getForceSum() - Method in class etomica.integrator.IntegratorVelocityVerlet
getFp8ShadeIndex(float, float, float) - Static method in class org.jmol.util.Shader
getfr(Potential2SoftSpherical, int, double, double) - Static method in class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
getfr(int, double, double, double, int, boolean) - Static method in class etomica.virial.B2Ionic
getfr(Potential2SoftSpherical, int, double, double) - Static method in class etomica.virial.B3ForSphericallySymmetricU
getfr(int, double, double) - Static method in class etomica.virial.B3LJ: Returns a discretized f function containing N points with a separation interval of del_r
getfr(int, double, double) - Static method in class etomica.virial.B4FFTLJ
getfr(int, double, double) - Static method in class etomica.virial.B5FFTLJ
getfr(int, double, double) - Static method in class etomica.virial.B6FFTLJ
getfr(int, double, double) - Static method in class etomica.virial.BnHNCLJ
getfr(int, double, double, Potential2Spherical) - Static method in class etomica.virial.BnIETP2Spherical
getfr(int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
getfr(Potential2Spherical, int, double, double, double) - Static method in class etomica.virial.BnPYCHe
getfr(int, double, double) - Static method in class etomica.virial.BnPYLJ
getfr(int, double, double) - Static method in class etomica.virial.BnSCALJ
getfr(IFunction) - Method in class etomica.virial.CalcFFT
getFrac() - Method in class etomica.normalmode.MCMoveHarmonicEin
getFrac() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
getFrac() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
getFrequencies() - Method in class etomica.action.CalcVibrationalModes: Calculates the frequencies (omegas) of wave vectors described by the eigenvalues (lambdas) of our system.
getFrequency(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager: Returns the trial frequency set for the given move, over and above the move's nominal frequency.
getFromBinFile(String) - Static method in class etomica.normalmode.ArrayReader2D: Deserializes a 3D array from the given file.
getFromFile(String, int) - Static method in class etomica.eigenstuff.ReaderIn
getFromFile(String) - Static method in class etomica.normalmode.ArrayReader1D
getFromFile(String, boolean) - Static method in class etomica.normalmode.ArrayReader1D
getFromFile(String) - Static method in class etomica.normalmode.ArrayReader2D: Returns 2D arrays from the given file.
getFromFile(String, int) - Static method in class etomica.normalmode.ArrayReader2D: Returns 2D arrays from the given file.
getFromFile(String) - Static method in class etomica.util.numerical.ArrayReader1D
getFromFile(String, boolean) - Static method in class etomica.util.numerical.ArrayReader1D
getFromNode(byte) - Method in interface etomica.graph.model.Graph
getFromNode(byte) - Method in class etomica.graph.model.impl.GraphImpl
getFType() - Method in class etomica.virial.Species7SiteRigidSF6
getFugacityFraction(int) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
getFugacityFraction() - Method in class etomica.integrator.mcmove.MCMoveSemigrand: Accessor method for the set of fugacity fractions.
getFullBondMask() - Method in class etomica.virial.ClusterSumHS
getFullBondMask() - Method in interface etomica.virial.ClusterWheatley: Returns number bond mask for all points for the configuration passed to checkConfig
getFullBondMask() - Method in class etomica.virial.ClusterWheatleyHS
getFullBondMask() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getFullOverlapResultForAlpha(double) - Method in class etomica.virial.overlap.DataVirialOverlap: Returns the full set of overlap results (averages and uncertainties for target and reference overlap averages).
getFullRatioResultForAlpha(double) - Method in class etomica.virial.overlap.DataVirialOverlap: Returns the full set of ratio results (reference and target ratios and errors on those ratios).
getFullRatioResultForAlpha(double, int) - Method in class etomica.virial.overlap.DataVirialOverlap
getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.ApiPlatform
getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
getFullSystemResult() - Method in class etomica.virial.overlap.DataVirialOverlap: Simply return the reference and target averages and uncertainties.
getFullSystemResult(int) - Method in class etomica.virial.overlap.DataVirialOverlap
getFunction() - Method in class etomica.data.DataSourceFunction
getFunction() - Method in class etomica.modifier.ModifierFunctionWrapper
getFunction() - Method in class etomica.util.numerical.Function1d
getFValues() - Method in class etomica.virial.ClusterSum
getFValues() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
getFValues() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
getFValues() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
getG() - Method in class etomica.modules.droplet.P1Smash
getG1() - Method in class etomica.graph.isomorphism.AbstractSearchState
getG1() - Method in interface etomica.graph.isomorphism.SearchState
getG2() - Method in class etomica.graph.isomorphism.AbstractSearchState
getG2() - Method in interface etomica.graph.isomorphism.SearchState
getG3D() - Method in class g3dsys.control.G3DSys: Get G3D
getG3DSys() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
getGamma() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
getGamma() - Method in class etomica.potential.P3BondAngleDreiding: Returns the characteristic energy of the potential
getGaussian() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
getGaussian() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
getGaussian() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
getGData() - Method in class org.jmol.g3d.Graphics3D: underlying GData object handles all general graphics setup.
getGlobalMoveInterval() - Method in class etomica.integrator.IntegratorManagerMC: Accessor method for the average interval between box-swap trials.
getGoal() - Method in class etomica.graph.traversal.AbstractTraversal
getGraphics() - Method in class etomica.graphics.EtomicaPlot
getGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
getGraphics(Object) - Method in class org.jmol.awt.Platform
getGroup3Count() - Static method in class org.jmol.viewer.JmolConstants
getGroup3List() - Static method in class org.jmol.viewer.JmolConstants
getGroupID(int[], int) - Static method in class etomica.virial.cluster.VirialDiagrams
getGroupID(int[], int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
getGroupingSize() - Method in class etomica.util.ScientificFormat
getGSum() - Method in class etomica.data.meter.PotentialCalculationRDF
getH() - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
getH() - Method in class etomica.spin.P1MagneticField
getH() - Method in class etomica.util.numerical.FiniteDifferenceDerivative
getH(int) - Method in class etomica.virial.cluster.ClusterOperations: Returns all diagrams of order n in the expansion for the total correlation function h(r), in the presence of any approximations currently in effect.
getHarmonicEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getHashmapAtomsetIterator() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getHashMapAtomTypeLikePairs() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getHashMapAtomTypesUnlikePairs() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
getHashMapPotentialIntraBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
getHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
getHeight() - Method in class etomica.graph.view.rasterizer.SVGConverter
getHeight() - Method in class org.jmol.util.JmolFont
getHelmholtzFreeEnergy(double) - Method in class etomica.normalmode.HarmonicCrystal
getHelmholtzFreeEnergy(double) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
getHelmholtzFreeEnergy(double) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
getHelmholtzFreeEnergy(double) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int, boolean) - Static method in class org.jmol.util.Hermite
getHexCode(short) - Static method in class org.jmol.util.Colix
getHexCodes(short[]) - Static method in class org.jmol.util.Colix
getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
getHexitValue(char) - Static method in class org.jmol.util.Escape
getHistogram() - Method in class etomica.data.DataHistogram
getHistogram() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
getHistogram() - Method in class etomica.mappedvirial.MeterMeanForce
getHistogram() - Method in interface etomica.util.Histogram: Returns the histogram as an array of doubles
getHistogram() - Method in class etomica.util.HistogramCollapsing
getHistogram() - Method in class etomica.util.HistogramDiscrete
getHistogram() - Method in class etomica.util.HistogramNotSoSimple
getHistogram() - Method in class etomica.util.HistogramReweightedData
getHistogram() - Method in class etomica.util.HistogramSimple
getHistogram2() - Method in class etomica.mappedvirial.MeterMeanForce
getHistograms() - Method in class etomica.data.AccumulatorHistogram
getHistory() - Method in class etomica.data.AccumulatorHistory
getHistory() - Method in interface etomica.util.History: Returns an array containing the y values that have been added to the History.
getHistory() - Method in class etomica.util.HistoryCollapsing: Returns the history
getHistory() - Method in class etomica.util.HistoryComplete: Returns an the history
getHistory() - Method in class etomica.util.HistoryScrolling: Returns an array with the most recent history at the end.
getHistoryLength() - Method in interface etomica.util.History: Returns the number of data points tracked by the History.
getHistoryLength() - Method in class etomica.util.HistoryCollapsing
getHistoryLength() - Method in class etomica.util.HistoryComplete
getHistoryLength() - Method in class etomica.util.HistoryScrolling
getHorizGBC() - Static method in class etomica.graphics.SimulationPanel
getHpType() - Method in class etomica.paracetamol.SpeciesParacetamol
getHType() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
getHType() - Method in class etomica.AlkaneEH.SpeciesMethane
getHType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
getHType() - Method in class etomica.models.traPPE.SpeciesMethanol
getHType() - Method in class etomica.virial.SpeciesAlkaneEH
getHType() - Method in class etomica.virial.SpeciesMethane
getHybridAcceptance() - Method in class etomica.integrator.IntegratorMD
getHydrogenType() - Method in class etomica.models.rowley.SpeciesEthanol
getHydrogenType() - Method in class etomica.models.rowley.SpeciesMethanol
getHydrogenType() - Method in class etomica.models.water.SpeciesWater3P
getHydrogenType() - Method in class etomica.models.water.SpeciesWater3POriented
getHydrogenType() - Method in class etomica.models.water.SpeciesWater4P
getHydrogenType() - Method in class etomica.models.water.SpeciesWater4PCOM
getHydrogenType() - Method in class etomica.models.water.SpeciesWater4POriented
getHydrophobicity(int) - Static method in class org.jmol.util.Elements
getHyType() - Method in class etomica.paracetamol.SpeciesParacetamol
getICPYCorrection(byte, boolean) - Static method in class etomica.virial.PYGenerator
getId() - Method in interface etomica.graph.model.Edge
getId() - Method in class etomica.graph.model.impl.EdgeImpl
getId() - Method in class etomica.graph.model.impl.NodeImpl
getId() - Method in interface etomica.graph.model.Node
getID() - Method in class etomica.virial.CoordinatePairLeafSet
getID() - Method in class etomica.virial.CoordinatePairMoleculeSet
getID() - Method in interface etomica.virial.CoordinatePairSet
getId() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
getId() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getId() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getId() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getId() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getId() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getId() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getId() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getId() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getId() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getId() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getID() - Method in class g3dsys.images.Figure: Get the ID of the figure
getIDataInfo(int) - Method in class etomica.normalmode.MeterTiltRotationHistogram
getIdealRefFraction(double) - Method in class etomica.overlap.DataOverlap: Returns the ideal fraction of time (or steps) spent in the reference system under the assumption that the current data while spending oldFrac amount of the calculation on the reference system.
getIdealRefFraction(double) - Method in interface etomica.overlap.IntegratorOverlap.ReferenceFracSource
getIdealRefFraction(double) - Method in class etomica.virial.overlap.DataSourceVirialOverlap
getIdealRefFraction(double) - Method in class etomica.virial.overlap.DataVirialOverlap
getIdealRefStepFraction() - Method in class etomica.overlap.IntegratorOverlap
getIgnoredAtomType() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getImageHeight(Object) - Method in interface org.jmol.api.ApiPlatform
getImageHeight(Object) - Method in class org.jmol.awt.Platform
getImagEigenvalues() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition: Return the imaginary parts of the eigenvalues
getImagEigenvalues() - Method in class org.jmol.util.Eigen: Return the imaginary parts of the eigenvalues
getImageShells() - Method in class etomica.graphics.DisplayBox
getImageWidth(Object) - Method in interface org.jmol.api.ApiPlatform
getImageWidth(Object) - Method in class org.jmol.awt.Platform
getImaginary() - Method in class etomica.util.FastFourierTransform
getImax() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
getIncludeHeader() - Method in class etomica.data.DataArrayWriter: Returns whether the writer includes column headers or not
getIncludeHeader() - Method in class etomica.data.DataTableWriter: Returns whether the writer includes column headers or not
getIndependentArrayDimension() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getIndependentArrayDimension() - Method in class etomica.data.DataSourceFunction
getIndependentArrayDimension() - Method in interface etomica.data.DataSourceIndependent: Returns the number of independent data dimensions
getIndependentArrayDimension() - Method in class etomica.data.DataSourceIndependentSimple
getIndependentArrayDimension() - Method in class etomica.data.DataSourcePoints
getIndependentArrayDimension() - Method in class etomica.data.DataSourceRmsVelocity
getIndependentArrayDimension() - Method in class etomica.data.meter.MeterDihedralAngle
getIndependentArrayDimension() - Method in class etomica.data.meter.MeterProfile
getIndependentArrayDimension() - Method in class etomica.data.meter.MeterProfileByAtoms
getIndependentArrayDimension() - Method in class etomica.data.meter.MeterProfileByVolume
getIndependentArrayDimension() - Method in class etomica.data.meter.MeterRDF
getIndependentArrayDimension() - Method in class etomica.data.meter.MeterRDFPC
getIndependentArrayDimension() - Method in class etomica.mappedvirial.MeterMeanForce
getIndependentArrayDimension() - Method in class etomica.metastable.DataProcessorXY
getIndependentArrayDimension() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getIndependentArrayDimension() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceFE
getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceFEHistogram
getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceImposedFEFit
getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourcePMu
getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourcePN
getIndependentArrayDimension() - Method in class etomica.normalmode.MeterAtomicDisplacement
getIndependentArrayDimension() - Method in class etomica.normalmode.MeterTiltHistogram
getIndependentArrayDimension() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
getIndependentData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
getIndependentData(int) - Method in class etomica.data.DataSourceFunction
getIndependentData(int) - Method in interface etomica.data.DataSourceIndependent: Returns the X data for the given dimension
getIndependentData(int) - Method in class etomica.data.DataSourceIndependentSimple
getIndependentData(int) - Method in class etomica.data.DataSourcePoints
getIndependentData(int) - Method in class etomica.data.DataSourceRmsVelocity
getIndependentData(int) - Method in class etomica.data.meter.MeterDihedralAngle
getIndependentData(int) - Method in class etomica.data.meter.MeterProfile
getIndependentData(int) - Method in class etomica.data.meter.MeterProfileByAtoms
getIndependentData(int) - Method in class etomica.data.meter.MeterProfileByVolume
getIndependentData(int) - Method in class etomica.data.meter.MeterRDF
getIndependentData(int) - Method in class etomica.data.meter.MeterRDFPC
getIndependentData(int) - Method in class etomica.mappedvirial.MeterMeanForce
getIndependentData(int) - Method in class etomica.metastable.DataProcessorXY
getIndependentData(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
getIndependentData(int) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
getIndependentData(int) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
getIndependentData(int) - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentData(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentData(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentData(int) - Method in class etomica.normalmode.DataSourceFE
getIndependentData(int) - Method in class etomica.normalmode.DataSourceFEHistogram
getIndependentData(int) - Method in class etomica.normalmode.DataSourceImposedFEFit
getIndependentData(int) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getIndependentData(int) - Method in class etomica.normalmode.DataSourcePMu
getIndependentData(int) - Method in class etomica.normalmode.DataSourcePN
getIndependentData(int) - Method in class etomica.normalmode.MeterAtomicDisplacement
getIndependentData(int) - Method in class etomica.normalmode.MeterTiltHistogram
getIndependentData(int) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
getIndependentDataInfo(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
getIndependentDataInfo(int) - Method in class etomica.data.DataSourceFunction
getIndependentDataInfo(int) - Method in interface etomica.data.DataSourceIndependent: Returns the DataInfo for the given dimension
getIndependentDataInfo(int) - Method in class etomica.data.DataSourceIndependentSimple
getIndependentDataInfo(int) - Method in class etomica.data.DataSourcePoints
getIndependentDataInfo(int) - Method in class etomica.data.DataSourceRmsVelocity
getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterDihedralAngle
getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterProfile
getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterProfileByAtoms
getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterProfileByVolume
getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterRDF
getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterRDFPC
getIndependentDataInfo(int) - Method in class etomica.mappedvirial.MeterMeanForce
getIndependentDataInfo(int) - Method in class etomica.metastable.DataProcessorXY
getIndependentDataInfo(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
getIndependentDataInfo(int) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceFE
getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceFEHistogram
getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceImposedFEFit
getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourcePMu
getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourcePN
getIndependentDataInfo(int) - Method in class etomica.normalmode.MeterAtomicDisplacement
getIndependentDataInfo(int) - Method in class etomica.normalmode.MeterTiltHistogram
getIndependentDataInfo(int) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
getIndependentTag() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getIndependentTag() - Method in class etomica.data.DataSourceFunction
getIndependentTag() - Method in interface etomica.data.DataSourceIndependent: Returns the tag associated with this DataSource.
getIndependentTag() - Method in class etomica.data.DataSourceIndependentSimple
getIndependentTag() - Method in class etomica.data.DataSourcePoints
getIndependentTag() - Method in class etomica.data.DataSourceRmsVelocity
getIndependentTag() - Method in class etomica.data.meter.MeterDihedralAngle
getIndependentTag() - Method in class etomica.data.meter.MeterProfile
getIndependentTag() - Method in class etomica.data.meter.MeterProfileByAtoms
getIndependentTag() - Method in class etomica.data.meter.MeterProfileByVolume
getIndependentTag() - Method in class etomica.data.meter.MeterRDF
getIndependentTag() - Method in class etomica.data.meter.MeterRDFPC
getIndependentTag() - Method in class etomica.mappedvirial.MeterMeanForce
getIndependentTag() - Method in class etomica.metastable.DataProcessorXY
getIndependentTag() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getIndependentTag() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
getIndependentTag() - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
getIndependentTag() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getIndependentTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getIndependentTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getIndependentTag() - Method in class etomica.normalmode.DataSourceFE
getIndependentTag() - Method in class etomica.normalmode.DataSourceFEHistogram
getIndependentTag() - Method in class etomica.normalmode.DataSourceImposedFEFit
getIndependentTag() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getIndependentTag() - Method in class etomica.normalmode.DataSourcePMu
getIndependentTag() - Method in class etomica.normalmode.DataSourcePN
getIndependentTag() - Method in class etomica.normalmode.MeterAtomicDisplacement
getIndependentTag() - Method in class etomica.normalmode.MeterTiltHistogram
getIndependentTag() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
getIndex() - Method in interface etomica.api.IAtom: Returns this IAtom's index, which is its place in the parent AtomGroup's list of child IAtoms.
getIndex() - Method in interface etomica.api.IAtomType: Returns the index for this IAtomType, within the context of an ISimulation.
getIndex() - Method in interface etomica.api.IBox: Returns the IBox's index.
getIndex() - Method in interface etomica.api.IBoxAtomIndexEvent
getIndex() - Method in interface etomica.api.IBoxIndexEvent
getIndex() - Method in interface etomica.api.IBoxMoleculeIndexEvent
getIndex() - Method in interface etomica.api.IMolecule: Returns this IMolecule's index, which is its place in the list of molecules of its ISpecies in its IBox.
getIndex() - Method in interface etomica.api.ISimulationAtomTypeIndexEvent
getIndex() - Method in interface etomica.api.ISimulationIndexEvent
getIndex() - Method in interface etomica.api.ISimulationSpeciesIndexEvent
getIndex() - Method in interface etomica.api.ISpecies: Returns the index for this ISpecies, within the context of an ISimulation.
getIndex() - Method in class etomica.atom.Atom
getIndex(IAtom) - Method in class etomica.atom.AtomToAtomSetFixed
getIndex(IAtom) - Method in interface etomica.atom.AtomToIndex: Returns an integer that this instance associates with the given atom.
getIndex(IAtom) - Method in class etomica.atom.AtomToIndexChild
getIndex() - Method in class etomica.atom.AtomTypeLeaf
getIndex() - Method in class etomica.atom.Molecule
getIndex(IMolecule) - Method in interface etomica.atom.MoleculeToIndex: Returns an integer that this instance associates with the given atom.
getIndex(IMolecule) - Method in class etomica.atom.MoleculeToMoleculeListSpecies
getIndex(IMolecule) - Method in class etomica.atom.MoleculeToMoleculeSetFixed
getIndex() - Method in class etomica.box.Box
getIndex() - Method in class etomica.box.BoxAtomIndexEvent
getIndex() - Method in class etomica.box.BoxIndexEvent
getIndex() - Method in class etomica.box.BoxMoleculeIndexEvent
getIndex() - Method in interface etomica.data.DataDistributer.Indexer
getIndex(double) - Method in class etomica.data.DataSourceUniform: Returns the index of the x value closest to the argument.
getIndex() - Method in class etomica.simulation.SimulationAtomTypeIndexEvent
getIndex() - Method in class etomica.simulation.SimulationIndexEvent
getIndex() - Method in class etomica.simulation.SimulationSpeciesIndexEvent
getIndex() - Method in class etomica.species.Species
getIndexed() - Method in class etomica.graph.view.rasterizer.SVGConverter
getIndexIterator() - Method in class etomica.space.Boundary
getIndexIterator() - Method in class etomica.space.BoundaryDeformablePeriodic
getIndexIterator() - Method in class etomica.space.BoundaryRectangularNonperiodic
getIndexIterator() - Method in class etomica.space.BoundaryRectangularPeriodic
getIndexIterator() - Method in class etomica.space.BoundaryRectangularPore
getIndexIterator() - Method in class etomica.space.BoundaryRectangularSlit
getIndexIterator() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
getIndexSelectedSpecies() - Method in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
getInflateDimensions() - Method in class etomica.data.meter.MeterPressureByVolumeChange: Accessor method for setInflateDimension.
getInfo() - Method in class org.jmol.util.Quaternion
getInnerIterator() - Method in class etomica.atom.iterator.ApiInnerVariable: Accessor method for the inner-loop atom iterator.
getInnerIterator() - Method in class etomica.atom.iterator.ApiIntergroup: Accessor method for the inner-loop atom iterator.
getInnerIterator() - Method in class etomica.atom.iterator.MpiInnerFixed: Accessor method for the inner-loop atom iterator.
getInnerIterator() - Method in class etomica.atom.iterator.MpiInnerVariable: Accessor method for the inner-loop atom iterator.
getInnerIterator() - Method in class etomica.graph.iterators.CartesianIterator
getInnerList() - Method in class etomica.atom.iterator.ApiInterArrayList: Returns the inner list used to generate the pairs.
getInnerList() - Method in class etomica.atom.iterator.MpiInterArrayList: Returns the inner list used to generate the pairs.
getInnerPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
getInnerRadius() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
getInnerRadius() - Method in class etomica.normalmode.P1Constraint
getInputFileName() - Method in class etomica.util.ReadParameters: Returns the fileName parameters are read from.
getInputFileName() - Method in class etomica.util.WriteParameters: Returns the fileName parameters are read from.
getInstance(int) - Static method in class etomica.space.Space: Returns a space instance of the given dimension, which must be 1, 2, or 3.
getInstance() - Static method in class etomica.space1d.Space1D
getInstance() - Static method in class etomica.space2d.Space2D
getInstance() - Static method in class etomica.space3d.Space3D
getInstance() - Static method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
getInstance() - Static method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
getInstance() - Static method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
getIntegrator() - Method in class etomica.action.ActionIntegrate
getIntegrator() - Method in class etomica.action.activity.ActivityIntegrate
getIntegrator() - Method in interface etomica.action.IntegratorAction
getIntegrator() - Method in class etomica.action.IntegratorActionAdapter
getIntegrator() - Method in interface etomica.api.IIntegratorEvent
getIntegrator() - Method in interface etomica.api.ISimulation: Returns the integrator for this simulation.
getIntegrator() - Method in class etomica.data.DataSourceTensorVirialHard
getIntegrator() - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
getIntegrator() - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
getIntegrator() - Method in class etomica.data.meter.MeterPressure: Returns the integrator associated with this instance.
getIntegrator() - Method in class etomica.data.meter.MeterPressureByVolumeChange: Returns the integrator associated with this instance.
getIntegrator() - Method in class etomica.data.meter.MeterPressureHard
getIntegrator() - Method in class etomica.data.meter.MeterPressureHardTensor
getIntegrator() - Method in class etomica.data.meter.MeterPressureMolecular: Returns the integrator associated with this instance.
getIntegrator() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
getIntegrator() - Method in class etomica.data.meter.MeterWidomInsertion: Returns the integrator associated with this class.
getIntegrator() - Method in class etomica.liquidLJ.MeterWidomInsertionP: Returns the integrator associated with this class.
getIntegrator() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
getIntegrator() - Method in class etomica.modules.mu.DataSourceWallPressureMu
getIntegrator() - Method in class etomica.normalmode.MeterPressureSuperBox: Returns the integrator associated with this instance.
getIntegrator() - Method in class etomica.simulation.Simulation: Returns the Simulation's primary integrator.
getIntegrator() - Method in class etomica.thermointegration.LjMc3D
getIntegratorMC() - Method in class etomica.integrator.IntegratorMD
getIntegratorOverlap() - Method in class etomica.normalmode.SimOverlapModule
getIntegrators() - Method in class etomica.integrator.IntegratorManagerMC
getInteractingList() - Method in class etomica.nbr.list.AtomPotentialList: Returns booleans indicating whether the Atom interacts with each potential or not.
getInteractingList() - Method in class etomica.nbr.list.molecule.MoleculePotentialList: Returns booleans indicating whether the Atom interacts with each potential or not.
getInteractionRange() - Method in class etomica.nbr.CriterionPositionWall: Returns the interaction range of the wall potential.
getInteractionRange() - Method in class etomica.nbr.CriterionSimple
getInteractionRange() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
getInteractionRangeDimension() - Method in class etomica.nbr.CriterionPositionWall
getInteractionRangeDimension() - Method in class etomica.nbr.CriterionSimple
getInteractionRangeDimension() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
getInteriorColor() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
getIntermolecularPotential() - Method in class etomica.parser.ParmedStructure: Gets the intermolecular PotentialGroup for the atom types found in this Structure.
getIntersection(Point3f, Vector3f, Point4f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
getIntersection(float, Point4f, Point3f[], List<Point3f[]>, float[], BitSet, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSurface
getIntersectionPP(Point4f, Point4f) - Static method in class org.jmol.util.Measure
getInterval() - Method in class etomica.data.DataPumpListener
getInterval() - Method in class etomica.data.DataPumpListenerPow
getInterval() - Method in class etomica.data.DataPumpListenerPowStrict
getInterval() - Method in class etomica.listener.IntegratorListenerAction
getIntialdisplaylist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getIntialpotentialdisplaylist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getIntraMolecularCriterion() - Method in class etomica.nbr.CriterionInterMolecular: Returns the intramolecular criterion, or null if none is in use.
getIntraPotentials(ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
getIntraPotentials(ISpecies) - Method in class etomica.nbr.PotentialMasterNbr
getInverseNormix(short) - Static method in class org.jmol.util.Normix
getIsFluctuationFromAvg() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
getIsNewPair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
getIsNewPair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
getIsothermalButtonsVisibility() - Method in class etomica.graphics.DeviceThermoSlider
getIsothermalButtonsVisibility() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
getIsotopeNumber(short) - Static method in class org.jmol.util.Elements
getIterator() - Method in class etomica.chem.models.Model.PotentialAndIterator
getIterator() - Method in class etomica.data.DataSourceRmsVelocity
getIterator() - Method in class etomica.data.meter.MeterBondOrderParameterQ
getIterator() - Method in class etomica.data.meter.MeterKineticEnergy: Returns the iterator that defines the atoms summed for their kinetic energy.
getIterator() - Method in class etomica.data.meter.MeterLocalDensity
getIterator() - Method in class etomica.data.meter.MeterLocalMoleFraction
getIterator() - Method in class etomica.data.meter.MeterRadiusGyration: Accessor method for the iterator that generates the atom pairs used to tabulate the ROG
getIterator() - Method in class etomica.lattice.LatticeSum
getIterator() - Method in class etomica.lattice.LatticeSumCrystal
getIterator() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
getIterator() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
getIy() - Method in class etomica.util.numerical.AkimaSplineSmootherDy: calculate the cumulative integral of y, interpolating dy/dx with a spline curve
getJacobian() - Method in class etomica.normalmode.CalcJacobian
getJavaInitializationString() - Method in class etomica.graphics.DimensionedDoubleEditor: Returns value in simulation units.
getJmax() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
getJSpinnerCountOfSpecies(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getJump() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
getJump() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
getK() - Method in class etomica.lattice.LatticeSum
getK() - Method in class etomica.lattice.LatticeSumCrystal
getK() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
getK() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
getKappa() - Method in class etomica.yukawa.P2Yukawa: Accessor methods for size and energy parameters.
getKinetic() - Method in class etomica.data.meter.MeterEnergy
getKineticEnergy() - Method in class etomica.data.meter.MeterEnergy
getKineticEnergy() - Method in class etomica.integrator.IntegratorMD
getL() - Method in class etomica.data.meter.MeterBondOrderParameterQ
getLabel() - Method in class etomica.action.ActionToggle: Returns the true or false label, depending on the current state of the toggle.
getLabel() - Method in class etomica.data.DataInfo
getLabel() - Method in class etomica.data.DataInfoFactory: Returns the label
getLabel() - Method in interface etomica.data.IDataInfo
getLabel() - Method in interface etomica.data.IEtomicaDataInfoFactory: Returns the label
getLabel() - Method in class etomica.graphics.DeviceBox
getLabel() - Method in class etomica.graphics.DeviceButton
getLabel() - Method in class etomica.graphics.DeviceSelector
getLabel() - Method in class etomica.graphics.DeviceSlider
getLabel() - Method in class etomica.graphics.DeviceSpinner
getLabel() - Method in class etomica.graphics.DeviceThermoSelector
getLabel() - Method in class etomica.graphics.Display: Accessor method of the label describing the display.
getLabel() - Method in class etomica.graphics.DisplayTextBox
getLabel() - Method in class etomica.graphics.DisplayTextBoxesCAE
getLabel() - Method in interface etomica.modifier.Modifier: Returns a descriptive label of the property being modified.
getLabel() - Method in class etomica.modifier.ModifierGeneral
getLabel() - Method in class etomica.modifier.ModifierNMolecule
getLabel() - Method in class etomica.modules.adsorption.ModifierPMu
getLabel() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
getLabel() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
getLabel() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
getLabel() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
getLabel() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
getLabel() - Method in class etomica.modules.entropylottery.ModifierDimensions
getLabel() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
getLabel() - Method in class etomica.modules.pistoncylinder.ActionPistonUpdate
getLabel() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
getLabel() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
getLabel() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
getLabel() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
getLabel() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
getLabel() - Method in class etomica.normalmode.ModifierCells3D
getLabel() - Method in class etomica.normalmode.ModifierXCells2D
getLabel() - Method in class etomica.normalmode.ModifierYCells2D
getLabel() - Method in class etomica.virial.simulations.ModifierTPI
getLabel() - Method in class etomica.zeolite.DeviceButtonSingle
getLabelPosition() - Method in class etomica.graphics.DeviceBox
getLabelPosition() - Method in class etomica.graphics.DisplayTextBox
getLabels() - Method in class etomica.graphics.DeviceTernarySelector: Accessor method for the labels.
getLabelType() - Method in class etomica.graphics.DeviceBox
getLabelType() - Method in class etomica.graphics.DisplayTextBox
getLambda() - Method in class etomica.modules.catalysis.P2SquareWellBonding: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.modules.catalysis.P2SquareWellSurface: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.modules.mu.P2SquareWellOneSide: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
getLambda() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
getLambda() - Method in class etomica.potential.P2DoubleWell: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.potential.P2PenetrableSquareWell: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.potential.P2SquareWell: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.potential.P2SquareWellRobust: Accessor method for well-diameter multiplier.
getLambda() - Method in class etomica.potential.P2TriangleWell
getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
getLambdaDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
getLambdaDimension() - Method in class etomica.potential.P2DoubleWell
getLambdaDimension() - Method in class etomica.potential.P2PenetrableSquareWell
getLambdaDimension() - Method in class etomica.potential.P2SquareWell
getLambdaDimension() - Method in class etomica.potential.P2SquareWellRobust
getLambdaDimension() - Method in class etomica.potential.P2TriangleWell
getLambdas() - Method in class etomica.action.CalcVibrationalModes: Performs an eigenvalue decomposition of the NxN matrix, fC.
getLanguage() - Method in class etomica.graph.view.rasterizer.SVGConverter
getLastA() - Method in class etomica.normalmode.WriteS
getLastBestParam() - Method in class etomica.modules.interfacial.FitTanh
getLastBestParam() - Method in class etomica.surfacetension.FitTanh
getLastCPairID() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getLastDMu() - Method in class etomica.normalmode.DataSourceMuRoot
getLastDPressure() - Method in class etomica.normalmode.DataSourceMuRoot
getLastDPressure() - Method in class etomica.normalmode.DataSourceMuRootPMatch
getLastGamma() - Method in class etomica.math.Gamma: Return the normalized complementary incomplete gamma function from the last calculation.
getLastGammaStar() - Method in class etomica.math.Gamma: Return the normalized incomplete gamma function from the last calculation.
getLastLine() - Method in class etomica.graph.engine.ConsoleUI
getLastLnTot() - Method in class etomica.normalmode.DataSourceMuRoot
getLastLnTot() - Method in class etomica.normalmode.DataSourceMuRootPMatch
getLastPolarizationEnergy() - Method in class etomica.models.co2.PNCO2GCPM
getLastPolarizationEnergy() - Method in class etomica.models.co2.PNGCPM
getLastPolarizationEnergy() - Method in class etomica.models.water.PNWaterGCPM
getLastPolarizationEnergy() - Method in interface etomica.potential.PotentialPolarizable: Returns the polarization energy from the last call to energy(AtomSet).
getLastPressure() - Method in class etomica.normalmode.DataSourceMuRoot
getLastPressure() - Method in class etomica.normalmode.DataSourceMuRoot1
getLastPressure() - Method in class etomica.normalmode.DataSourceMuRootPMatch
getLastTotalEnergy() - Method in class etomica.normalmode.MCMoveHarmonic: Returns the harmonic energy of the configuration based on the last harmonic move made by this MC Move.
getLastVacancyConcentration() - Method in class etomica.normalmode.DataSourceMuRoot
getLastVacancyConcentration() - Method in class etomica.normalmode.DataSourceMuRoot1
getLastVacancyConcentration() - Method in class etomica.normalmode.DataSourceMuRootPMatch
getLastValue() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
getLastValues() - Method in class etomica.virial.cluster.ClusterDiagramTree
getLattice() - Method in interface etomica.box.BoxCellManager: Returns the lattice that defines the cell arrangement.
getLattice() - Method in class etomica.lattice.LatticeSum
getLattice() - Method in class etomica.lattice.LatticeSumCrystal
getLattice() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Returns the lattice from which the iterates are given.
getLattice() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
getLattice() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
getLattice() - Method in class etomica.nbr.cell.NeighborCellManager
getLattice() - Method in class etomica.nbr.site.NeighborSiteManager: Returns the lattice used to define the neighbor structure.
getLattice() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
getLatticeAMemento() - Method in class etomica.config.GrainBoundaryConfiguration: Returns a lattice with positions the same as those used in the most recent use of initializeCoordinates.
getLatticeArrayIndex() - Method in class etomica.nbr.cell.Cell
getLatticeArrayIndex() - Method in class etomica.nbr.cell.molecule.CellMolecular
getLatticeArrayIndex() - Method in class etomica.nbr.site.AtomSite
getLatticeBMemento() - Method in class etomica.config.GrainBoundaryConfiguration
getLatticeConstant() - Method in interface etomica.lattice.CubicLattice: Accesses the size of the unit cell, the length of each edge of a single cell.
getLatticeConstant() - Method in class etomica.lattice.LatticeCubicBcc
getLatticeConstant() - Method in class etomica.lattice.LatticeCubicDiamond
getLatticeConstant() - Method in class etomica.lattice.LatticeCubicFcc
getLatticeConstant() - Method in class etomica.lattice.LatticeCubicSimple
getLatticeConstants() - Method in class etomica.config.ConfigurationLattice.MyLattice
getLatticeConstants() - Method in class etomica.lattice.BravaisLattice
getLatticeConstants() - Method in interface etomica.lattice.SpaceLattice
getLatticeConstants() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
getLatticeConstants() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
getLatticeCorrec() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
getLatticeEnergy() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getLatticeEnergy() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
getLatticeEnergy() - Method in class etomica.normalmode.HarmonicCrystal
getLatticeEnergy() - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
getLatticeEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
getLatticeEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getLatticeEnergy() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getLatticeEnergy() - Method in class etomica.normalmode.MeterOverlapSwitch
getLatticeEnergy() - Method in class etomica.normalmode.MeterTargetTP
getLatticeEnergy() - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
getLatticeEnergy() - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
getLatticeEnergy() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
getLatticeMemento() - Method in class etomica.config.ConfigurationLattice: Returns a lattice with positions the same as those used in the most recent use of initializeCoordinates.
getLatticeMemento() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice: Returns a lattice with positions the same as those used in the most recent use of initializeCoordinates.
getLatticeMemento() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice: Returns a lattice with positions the same as those used in the most recent use of initializeCoordinates.
getLatticePosition(IAtom) - Method in class etomica.normalmode.CoordinateDefinition
getLatticePosition(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
getLatticePosition(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
getLayers() - Method in class g3dsys.images.ImageShell: Gets the number of image shell layers
getLeafIndex() - Method in interface etomica.api.IAtom: Returns the global index (within the Box) of this Atom.
getLeafIndex() - Method in class etomica.atom.Atom
getLeafList() - Method in interface etomica.api.IBox: Returns the list of atoms contained in this box.
getLeafList() - Method in class etomica.box.Box
getLeafType() - Method in class etomica.species.SpeciesSpheres
getLeafType() - Method in class etomica.species.SpeciesSpheresMono
getLength() - Method in interface etomica.data.IData: Returns the number of values held by the data instance.
getLength() - Method in interface etomica.data.IDataInfo: Returns the number of numerical values held by the IData object.
getLength() - Method in class etomica.data.types.DataDouble.DataInfoDouble
getLength() - Method in class etomica.data.types.DataDouble: Returns 1, indicating that this data object holds one value.
getLength() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray: Returns the total number of elements in the constructed DataDoubleArray.
getLength() - Method in class etomica.data.types.DataDoubleArray: Returns the total length of the wrapped array.
getLength() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray: Returns the total number of elements in the constructed DataDoubleArray.
getLength() - Method in class etomica.data.types.DataDoubleBDArray: Returns the total length of the wrapped array.
getLength() - Method in class etomica.data.types.DataGroup.DataInfoGroup
getLength() - Method in class etomica.data.types.DataGroup
getLength() - Method in class etomica.data.types.DataTable: Returns the number of values held by the data instance.
getLength() - Method in class etomica.data.types.DataTensor.DataInfoTensor
getLength() - Method in class etomica.data.types.DataTensor: Returns the number of elements in the wrapped tensor.
getLength() - Method in class etomica.data.types.DataVector.DataInfoVector
getLength() - Method in class etomica.data.types.DataVector: Returns the number of elements in the wrapped vector.
getLength() - Method in class etomica.math.geometry.LineSegment
getLengthAlkaneChain(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getLevel(int) - Static method in class org.jmol.util.Logger: Returns the text corresponding to a level.
getLightSource() - Static method in class org.jmol.util.GData
getLiquidColor() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
getLiquidFilter() - Method in class etomica.modules.droplet.P2Cohesion
getList() - Method in class etomica.atom.iterator.ApiIntraArrayList: Returns the list used to generate the pairs.
getList() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
getList() - Method in class etomica.atom.iterator.MpiIntraArrayList: Returns the list used to generate the pairs.
getList() - Method in class org.jmol.script.ScriptVariable
getLnBias(int) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
getLnBiasDiff() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
getLoad() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
getLocale() - Static method in class etomica.graph.view.rasterizer.Messages: Implements Localizable.getLocale().
getLocalVisitor() - Method in class etomica.graph.traversal.AbstractTraversal
getLogAverage(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getLogAverage(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapLogAvg
getLogAverageAndError(double) - Method in class etomica.overlap.DataOverlap: Returns the natural log of the average ratio and its uncertainty for the given value of alpha
getLogAverageAndError(boolean, double) - Method in class etomica.overlap.DataOverlap: Returns the natural log of the average value from the reference or target system (as specified) and its uncertainty for the given value of alpha
getLogError(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getLogError(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapLogAvg
getLogError(int) - Method in class etomica.overlap.DataOverlap: Returns the uncertainty in the log of the average corresponding to the iAlpha value of alpha.
getLogLevel() - Static method in class org.jmol.util.Logger
getLowerLimit() - Method in class etomica.models.hexane.SpeciesHexane
getLxy() - Method in class etomica.interfacial.ConfigurationLammps
getMakeLrc() - Method in class etomica.potential.P2SoftSphericalTruncated
getMass() - Method in interface etomica.api.IAtomType: Returns the value of the mass.
getMass() - Method in interface etomica.api.IElement
getMass() - Method in class etomica.atom.AtomTypeLeaf
getMass() - Method in class etomica.chem.elements.Element
getMass() - Method in class etomica.chem.elements.ElementChemical
getMass() - Method in class etomica.chem.elements.ElementSimple
getMass() - Method in class etomica.potential.P1HardMovingBoundary
getMass(IMolecule) - Method in interface etomica.potential.P2SemiclassicalMolecular.MoleculeInfo: Returns the mass of the molecule.
getMass(IMolecule) - Method in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
getMass() - Method in interface etomica.species.ISpeciesOriented
getMass() - Method in class etomica.species.SpeciesOriented
getMass() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
getMass() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
getMass() - Method in class etomica.units.systems.LJ
getMassDimension() - Method in class etomica.atom.AtomTypeLeaf
getMassDimension() - Method in class etomica.chem.elements.Element
getMassDimension() - Method in class etomica.potential.P1HardMovingBoundary
getMassDimension() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
getMathContext() - Method in class etomica.virial.MeterVirialBDBin
getMathContext() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
getMathContext() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
getMatrix() - Method in class org.jmol.util.Quaternion
getMatrixFromFile(String, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
getMatrixFromFile(String, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
getMaxBlocks() - Method in class etomica.data.AccumulatorAverageCollapsing
getMaxBonds() - Method in class etomica.association.AssociationHelperBranched
getMaxBonds() - Method in class etomica.association.AssociationHelperMolecule
getMaxDistance() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
getMaxDistance() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
getMaxElement() - Method in class etomica.lattice.IndexIteratorTriangular
getMaxElement() - Method in class etomica.lattice.LatticeSum
getMaxElementMin() - Method in class etomica.lattice.IndexIteratorTriangular
getMaxHeight() - Method in class etomica.graph.view.rasterizer.SVGConverter
getMaximum() - Method in class etomica.graphics.DeviceSlider
getMaximum() - Method in class etomica.graphics.DeviceSpinner
getMaximumFractionDigits() - Method in class etomica.util.ScientificFormat
getMaximumIntegerDigits() - Method in class etomica.util.ScientificFormat
getMaximumSeparation() - Method in class etomica.potential.P2Fene: Accessor method for harmonic energy parameter
getMaximumSeparationDimension() - Method in class etomica.potential.P2Fene
getMaxIndex() - Method in class etomica.box.BoxGlobalAtomIndexEvent
getMaxIterations() - Method in class etomica.integrator.IntegratorVelocityVerletShake
getMaxLatticeShell() - Method in class etomica.lattice.LatticeSumCrystal
getMaxLatticeShell() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
getMaxLatticeShell() - Method in class etomica.normalmode.HarmonicCrystal
getMaxLatticeShell() - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
getMaxLatticeShell() - Method in class etomica.normalmode.NormalModesPotential
getMaxLatticeShell() - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
getMaxLatticeShell() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
getMaxLatticeShell() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
getMaxLatticeShell() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getMaxNbrsVapor() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
getMaxPotentialRange() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Returns the maximum range of any potential held by this potential master
getMaxPotentialRange() - Method in class etomica.nbr.list.PotentialMasterList: Returns the maximum range of any potential held by this potential master
getMaxSleep() - Method in class etomica.graphics.DeviceDelaySlider
getMaxSteps() - Method in class etomica.action.ActionIntegrate: Accessor method for the number of doStep calls to be performed by this integrator after it is started.
getMaxSteps() - Method in class etomica.action.activity.ActivityIntegrate: Accessor method for the number of doStep calls to be performed by this integrator after it is started.
getMaxWidth() - Method in class etomica.graph.view.rasterizer.SVGConverter
getMaxWidth() - Method in class etomica.util.ScientificFormat
getMaxX() - Method in class g3dsys.control.G3DSys
getMaxY() - Method in class g3dsys.control.G3DSys
getMaxZ() - Method in class g3dsys.control.G3DSys
getMCMove() - Method in class etomica.integrator.mcmove.MCMoveEvent
getMCMove() - Method in class etomica.integrator.mcmove.MCMoveTrialCompletedEvent
getMCMove() - Method in class etomica.integrator.mcmove.MCMoveTrialFailedEvent
getMCMove() - Method in class etomica.integrator.mcmove.MCMoveTrialInitiatedEvent
getMCMoveClusterTorsionMulti() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getMCMoveMoleculeExchange() - Method in class etomica.integrator.IntegratorGEMC: Returns the object that performs the molecule-exchange move in the GE simulation.
getMCMoves() - Method in class etomica.integrator.mcmove.MCMoveManager: Constructs and returns array of all moves added to the integrator.
getMCMoveVolumeExchange() - Method in class etomica.integrator.IntegratorGEMC: Returns the object that performs the volume-exchange move in the GE simulation.
getMediaType() - Method in class etomica.graph.view.rasterizer.SVGConverter
getMembraneDim() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getMembraneDim() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: The dimension of the membrane (0=x, 1=y, 2=z).
getMembraneThickness() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: Returns the thickness (angstroms) of each layer of the membrane (see getNumMembraneLayers)
getMembraneThicknessPerLayer() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getMembraneWidth() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getMembraneWidth() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: Returns the width of the membrane.
getMessage() - Method in exception etomica.graph.view.rasterizer.SVGConverterException
getMetadata() - Method in interface etomica.graph.model.Edge
getMetadata() - Method in class etomica.graph.model.impl.EdgeImpl
getMetadata() - Method in class etomica.graph.model.impl.NodeImpl
getMetadata() - Method in interface etomica.graph.model.Node
getMeter() - Method in class etomica.graphics.DisplayScrollingGraph: Accessor method for the meter that generates the displayed value.
getMeterPotentialEnergy() - Method in class etomica.integrator.IntegratorBox
getMeterTemperature() - Method in class etomica.integrator.IntegratorMD: returns the temperature meter used for velocity rescaling.
getMillerIndex(int) - Method in class etomica.lattice.LatticePlane: Returns the current value of the i-th Miller index.
getMinBondedAtomDistance() - Method in class etomica.association.AssociationHelperBranched
getMinBondedAtomDistance() - Method in class etomica.association.AssociationHelperDouble
getMinBondedMoleculeDistance() - Method in class etomica.association.AssociationHelperMolecule
getMinimum() - Method in class etomica.graphics.DeviceSlider
getMinimum() - Method in class etomica.graphics.DeviceSpinner
getMinimumFractionDigits() - Method in class etomica.util.ScientificFormat
getMinimumIntegerDigits() - Method in class etomica.util.ScientificFormat
getMinNumAtoms() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
getMinRadicalSites() - Method in class etomica.modules.catalysis.P2SquareWellSurface
getMinX() - Method in class g3dsys.control.G3DSys
getMinY() - Method in class g3dsys.control.G3DSys
getMinZ() - Method in class g3dsys.control.G3DSys
getMobileSpecies() - Method in class etomica.config.GrainBoundaryTiltConfiguration
getModelSelectedSpecies() - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
getModelSpeciesSelection() - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
getModeNum() - Method in class etomica.normalmode.MCMoveHarmonic
getModeSigns() - Method in class etomica.action.CalcVibrationalModes: Returns a one dimensional array of length 3 with the total number of positive, negative, and imaginary modes.
getModifier() - Method in class etomica.action.ActionToggle: Returns the boolean modifier used by this action.
getModifier() - Method in class etomica.graphics.DeviceBox: Accessor method for the modifier that receives the edit.
getModifier() - Method in class etomica.graphics.DeviceCheckBox: Specifies the boolean modifier that is set between true and false by the button.
getModifier() - Method in class etomica.graphics.DeviceSlider
getModifier() - Method in class etomica.graphics.DeviceSpinner
getModifier() - Method in class etomica.graphics.DeviceThermoSlider
getModifier() - Method in class etomica.graphics.DeviceToggleRadioButtons: Specifies the boolean modifier that is set between true and false by the button.
getModifier() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
getModifier() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
getModifier() - Method in class etomica.normalmode.DeviceWaveVectorSlider
getMolecularModelDisplayName() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getMolecule() - Method in interface etomica.api.IBoxMoleculeEvent
getMolecule(int) - Method in interface etomica.api.IMoleculeList: Returns the i-th atom, with numbering beginning from 0.
getMolecule() - Method in class etomica.association.MoleculeSourceRandomDimer
getMolecule() - Method in class etomica.association.MoleculeSourceRandomMonomer
getMolecule() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet
getMolecule(int) - Method in class etomica.atom.MoleculeArrayList
getMolecule(int) - Method in class etomica.atom.MoleculeListWrapper: Part of implementation of AtomSet interface.
getMolecule(int) - Method in class etomica.atom.MoleculePair
getMolecule(int) - Method in class etomica.atom.MoleculesetArray: Part of implementation of AtomSet interface.
getMolecule(int) - Method in class etomica.atom.MoleculeSetSinglet
getMolecule() - Method in interface etomica.atom.MoleculeSource: Returns an atom.
getMolecule() - Method in class etomica.atom.MoleculeSourceRandomMolecule: returns a random molecule from the box
getMolecule(int) - Method in class etomica.box.AtomSetAllMolecules
getMolecule() - Method in class etomica.box.BoxMoleculeEvent
getMoleculeAgentClass() - Method in class etomica.association.AssociationManagerMolecule
getMoleculeAgentClass() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
getMoleculeAgentClass() - Method in interface etomica.atom.MoleculeAgentManager.MoleculeAgentSource: Returns the Class of the agent.
getMoleculeAgentClass() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
getMoleculeAgentClass() - Method in class etomica.graphics.ColorSchemeRandomByMolecule
getMoleculeAgentClass() - Method in class etomica.integrator.IntegratorRigidIterative
getMoleculeAgentClass() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
getMoleculeAgentClass() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
getMoleculeAgentClass() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
getMoleculeAgentClass() - Method in class etomica.modules.rosmosis.MeterFlux
getMoleculeAgentClass() - Method in class etomica.modules.sam.CriterionTether3
getMoleculeAgentClass() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
getMoleculeAgentClass() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getMoleculeAgentClass() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
getMoleculeAgentClass() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
getMoleculeAgentClass() - Method in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
getMoleculeAgentClass() - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
getMoleculeAgentClass() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
getMoleculeAgentClass() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
getMoleculeCount() - Method in interface etomica.api.IMoleculeList
getMoleculeCount() - Method in class etomica.atom.MoleculeArrayList
getMoleculeCount() - Method in class etomica.atom.MoleculeListWrapper: Returns the length of the wrapped array.
getMoleculeCount() - Method in class etomica.atom.MoleculePair
getMoleculeCount() - Method in class etomica.atom.MoleculesetArray: Returns the length of the wrapped array.
getMoleculeCount() - Method in class etomica.atom.MoleculeSetSinglet
getMoleculeCount() - Method in class etomica.box.AtomSetAllMolecules
getMoleculeDataInfo() - Method in interface etomica.data.DataSourceMolecular
getMoleculeDataInfo() - Method in class etomica.data.meter.MeterNMolecules
getMoleculeDataInfo() - Method in class etomica.modules.interfacial.MeterOrientation
getMoleculeDisplayName() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getMoleculeList(ISpecies) - Method in interface etomica.api.IBox: Returns the list of molecules of the given species as an IAtomSet that are in this box.
getMoleculeList() - Method in interface etomica.api.IBox: Returns a list of all molecules in this box as an IAtomSet.
getMoleculeList(IMolecule) - Method in interface etomica.atom.MoleculeToMoleculeList: Returns the ArrayList that this instance associates with the given atom.
getMoleculeList(IMolecule) - Method in class etomica.atom.MoleculeToMoleculeListSpecies
getMoleculeList(IMolecule) - Method in class etomica.atom.MoleculeToMoleculeSetFixed
getMoleculeList(ISpecies) - Method in class etomica.box.Box
getMoleculeList() - Method in class etomica.box.Box
getMoleculeListDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getMoleculeListDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getMoleculeListDisplayString() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getMoleculeListDisplayTable() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getMoleculeListDisplayTable() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getMoleculeListDisplayTM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getMoleculeListDisplayTM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getMoleculeOffset() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getMoleculeOffset() - Method in class etomica.modules.sam.ConfigurationSAM
getMoleculeOrientation(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
getMoleculeOrientation(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
getMoleculeOrientation(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer: return the initial Orientation of the molecule
getMolecules() - Method in class etomica.parser.ParmedStructure: Gets the list of all molecules in the Structure, initialized with their coordinates in space.
getMolecules(IBox) - Static method in class etomica.util.Debug: Returns an AtomPair containing the two atoms with global indices ATOM1_INDEX and ATOM2_INDEX within the given box.
getMoleculeSource() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange: Returns the AtomSource this class uses to pick molecules to delete.
getMoleculeSource() - Method in class etomica.models.hexane.MCMoveCBMC: Returns the AtomSource used to select Atoms acted on by MC trials.
getMoment() - Method in class etomica.modules.vle.VLESim
getMoment(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getMoment(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getMoment(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getMomentAndAxes(IAtomOriented) - Method in interface etomica.potential.P2SemiclassicalAtomic.AtomInfo: Returns the moment of inertia as a vector containing Ix, Iy, Iz and also the principle axes.
getMomentAndAxes(IMolecule) - Method in interface etomica.potential.P2SemiclassicalMolecular.MoleculeInfo: Returns the moment of inertia as a vector containing Ix, Iy, Iz and also the principle axes.
getMomentAndAxes(IMolecule) - Method in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
getMomentOfInertia() - Method in class etomica.atom.AtomTypeOrientedSphere
getMomentOfInertia() - Method in interface etomica.atom.IAtomTypeOriented: Returns the principle components of the moment of inertia of the atom within the body-fixed frame.
getMomentOfInertia() - Method in interface etomica.species.ISpeciesOriented: Returns the principle components of the moment of inertia of the molecule within the body-fixed frame.
getMomentOfInertia() - Method in class etomica.species.SpeciesOriented
getMomentOfInertia() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
getMomentSquare(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getMonomerColor() - Method in class etomica.association.ColorSchemeSmer: Returns the color used for all dimers.
getMove() - Method in class etomica.data.DataSourceAcceptanceRatio
getMoveEventManager() - Method in class etomica.integrator.IntegratorManagerMC
getMoveEventManager() - Method in class etomica.integrator.IntegratorMC: Adds a listener that will be notified when a MCMove trial is attempted and when it is completed.
getMoveManager() - Method in class etomica.integrator.IntegratorManagerMC
getMoveManager() - Method in class etomica.integrator.IntegratorMC
getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
getMSMCGraphs(boolean, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
getMSMCGraphs(boolean, int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
getMSMCGraphs(boolean, int) - Method in class etomica.virial.cluster.VirialDiagramsPT
getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
getMSMCGraphsEX(boolean) - Method in class etomica.virial.cluster.ExternalVirialDiagrams
getMType() - Method in class etomica.models.water.SpeciesWater4P
getMType() - Method in class etomica.models.water.SpeciesWater4PCOM
getMType() - Method in class etomica.models.water.SpeciesWater4POriented
getMu() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Accessor method for the chemical potential of th insertion/deletion species.
getMuDimension() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Indicates that chemical potential has dimensions of energy.
getMultiBonds() - Method in class etomica.virial.ClusterBondsNonAdditive: Returns the list of multiBonds to multiply.
getN() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
getN() - Method in class etomica.potential.P4TorsionDreiding
getn() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
getN1() - Method in class etomica.graph.isomorphism.AbstractSearchState
getN1(byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
getN1() - Method in class etomica.graph.isomorphism.NodePair
getN2() - Method in class etomica.graph.isomorphism.AbstractSearchState
getN2(byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
getN2() - Method in class etomica.graph.isomorphism.NodePair
getName() - Method in class etomica.data.meter.MeterDihedralAngle
getName() - Method in class etomica.data.meter.MeterMomentumCOM
getName() - Method in class etomica.data.meter.MeterPositionCOM
getName() - Method in class etomica.data.meter.MeterPressureHardTensor
getName() - Method in class etomica.data.meter.MeterRDF
getName() - Method in class etomica.data.meter.MeterRDFPC
getName() - Method in class etomica.data.meter.MeterTensorVelocity
getName() - Method in class etomica.graph.engine.impl.PropertyImpl
getName() - Method in class etomica.graph.engine.impl.VariableImpl
getName() - Method in interface etomica.graph.engine.Parser.Property
getName() - Method in interface etomica.graph.engine.Parser.Variable
getName() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
getName() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
getName() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource: Returns the name of the source.
getName() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
getName() - Method in class etomica.graphics.EtomicaTheme
getName() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
getName() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
getName() - Method in class etomica.normalmode.MeterNormalMode
getName() - Method in enum org.jmol.constant.EnumStereoMode
getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
getNBennetPoints() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
getNBennetPoints() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
getNBins() - Method in class etomica.data.AccumulatorHistogram
getNBins() - Method in interface etomica.util.Histogram: Returns the number of bins in the histogram.
getNBins() - Method in class etomica.util.HistogramDiscrete
getNBins() - Method in class etomica.util.HistogramNotSoSimple
getNBins() - Method in class etomica.util.HistogramReweightedData
getNBins() - Method in class etomica.util.HistogramSimple
getNbrAtoms(IBox) - Method in class etomica.normalmode.P1ConstraintNbr
getNbrCellIterator() - Method in class etomica.nbr.cell.Api1ACell
getNbrCellIterator() - Method in class etomica.nbr.cell.ApiAACell
getNbrCellIterator() - Method in interface etomica.nbr.cell.AtomsetIteratorCellular
getNbrCellIterator() - Method in interface etomica.nbr.cell.molecule.MoleculesetIteratorCellular
getNbrCellIterator() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
getNbrCellIterator() - Method in class etomica.nbr.cell.molecule.MpiAACell
getNbrCellManager(IBox) - Method in class etomica.nbr.cell.PotentialMasterCell
getNbrCellManager(IBox) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
getNbrCellManager(IBox) - Method in class etomica.nbr.list.PotentialMasterList
getNbrCellManager(IBox) - Method in class etomica.nbr.PotentialMasterHybrid
getNbrCellManagerThreaded(IBox) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
getNbrDistance() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
getNCellModifier() - Method in class etomica.normalmode.DeviceCellNum3DSlider
getNCellNum() - Method in class etomica.normalmode.DeviceCellNum3DSlider
getNCellNum() - Method in class etomica.normalmode.NormalModes3D
getNCells() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
getNCells() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
getNCellsX() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getNCellsX() - Method in class etomica.modules.sam.ConfigurationSAM
getNCellsZ() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getNCellsZ() - Method in class etomica.modules.sam.ConfigurationSAM
getNCrossLinkersAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
getNData() - Method in class etomica.data.types.DataGroup: Returns the number of data objects encapsulated by this DataGroup.
getNDataInfo() - Method in class etomica.data.types.DataGroup.DataInfoGroup
getNDiAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
getNDiagrams() - Method in class etomica.virial.cluster.ClusterDiagramTree
getNDiol() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
getNegativePrefix() - Method in class etomica.util.ScientificFormat
getNegativeSuffix() - Method in class etomica.util.ScientificFormat
getNeighborCriteria() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
getNeighborCriteria() - Method in class etomica.nbr.list.PotentialMasterList
getNeighborDistance() - Method in class etomica.lattice.CellLattice.NeighborIterator
getNeighborManager(IBox) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
getNeighborManager(IBox) - Method in class etomica.nbr.list.PotentialMasterList
getNeighborManager(IBox) - Method in class etomica.nbr.PotentialMasterHybrid
getNeighborRange() - Method in class etomica.nbr.CriterionPositionWall
getNeighborRange() - Method in class etomica.nbr.CriterionSimple
getNeighborRange() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
getNeighborRangeDimension() - Method in class etomica.nbr.CriterionPositionWall
getNeighborRangeDimension() - Method in class etomica.nbr.CriterionSimple
getNeighborRangeDimension() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
getNewPartners() - Method in class etomica.potential.PotentialReactive.BondChangeData
getNGraft() - Method in class etomica.modules.colloid.ConfigurationColloid
getNInsert() - Method in class etomica.data.meter.MeterWidomInsertion: Accessor to number of Widom insertions attempted with each call to currentValue
getNInsert() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Accessor to number of Widom insertions attempted with each call to currentValue
getNInsert() - Method in class etomica.liquidLJ.MeterWidomInsertionP: Accessor to number of Widom insertions attempted with each call to currentValue
getNitrogenType() - Method in class etomica.models.nitrogen.SpeciesN2
getNitrogenType() - Method in class etomica.models.nitrogen.SpeciesN2B
getNitrogenType() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
getNMajor() - Method in class etomica.graphics.DeviceSlider
getNMinor() - Method in class etomica.graphics.DeviceSlider
getNMolecules(ISpecies) - Method in interface etomica.api.IBox: Returns the number of molecules in this box of the given ISpecies.
getNMolecules(ISpecies) - Method in class etomica.box.Box
getNMonoAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
getNMonoOl() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
getNode(byte) - Method in interface etomica.graph.model.Graph
getNode(byte) - Method in class etomica.graph.model.impl.GraphImpl
getNoisyAdjustment() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
getNominalFluctuation() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
getNominalFrequency() - Method in class etomica.integrator.mcmove.MCMove: Returns a nominal, unnormalized frequency for performing this move, relative to the other moves that have been added to the integrator.
getNonBondedInteractionModel() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getNoneCliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
getNoneCliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
getNonPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNCO2GCPM: This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)
getNonPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM: This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)
getNonPolarizationEnergy(IMoleculeList) - Method in class etomica.models.water.PNWaterGCPM: This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)
getNoOfSpheres() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
getNoOfSteps() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getNoOfSteps() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
getNoOfStepsField() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getNorm() - Method in class etomica.math.Quaternion: Returns the norm of the Quaternion q defined as N = sqrt(q*q)
getNormal(IVectorMutable) - Method in class etomica.models.hexane.CBMCGrowSolidHexane: Returns a unit normal to the argument vector
getNormal() - Method in class org.jmol.util.Quaternion
getNormalDirected(Vector3f) - Method in class org.jmol.util.Quaternion
getNormalFromCenter(Point3f, Point3f, Point3f, Point3f, boolean, Vector3f) - Static method in class org.jmol.util.Measure
getNormalModes() - Method in class etomica.normalmode.HarmonicCrystal
getNormalModes() - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
getNormalModes() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
getNormalModes() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getNormalThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
getNormalToLine(Point3f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
getNormixCount() - Static method in class org.jmol.util.Normix
getNormixV(Vector3f, BitSet) - Static method in class org.jmol.util.Normix
getnPoints() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getnReactCO() - Method in class etomica.modules.catalysis.ReactionManagerCO
getNRows() - Method in class etomica.data.types.DataTable.DataInfoTable: Returns the number of rows in the table
getNRows() - Method in class etomica.data.types.DataTable.DataInfoTableFactory: Returns the number of rows.
getNRows() - Method in class etomica.data.types.DataTable: Returns the number of rows in each and every column of the table.
getNSpheres() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getNSpheres() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getNthSpeciesAdded() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getNthSpeciesSelectedIndex() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getNTicks() - Method in class etomica.graphics.DisplayScrollingGraph
getNType() - Method in class etomica.paracetamol.SpeciesParacetamol
getNullPotential(IAtomType) - Method in class etomica.integrator.IntegratorHard
getNumAlpha() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getNumAlpha() - Method in interface etomica.overlap.AlphaSource: Returns the number of possible alpha values.
getNumAlpha() - Method in class etomica.overlap.MeterOverlap
getNumAlpha() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
getNumAlpha() - Method in class etomica.virial.simulations.SimulationVirialOverlap: Returns the number of alpha values used for the production stage of the simulation
getNumAlpha() - Method in class etomica.virial.simulations.SimulationVirialOverlap2: Returns the number of alpha values used for the production stage of the simulation
getNumAtoms() - Method in class etomica.chem.models.ModelChain: Returns the number of atoms per chain molecule.
getNumAtoms() - Method in class etomica.zeolite.ConfigurationFileXYZ
getNumBeads() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
getNumber() - Method in class etomica.modules.materialfracture.StrainColorScheme
getNumberFraction() - Method in class etomica.species.SpeciesSpheresHetero: Returns the number fraction of each child type created by this factory.
getNumberOfTrials() - Method in class etomica.models.hexane.MCMoveCBMC
getNumCO() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getNumCollapseBins() - Method in class etomica.util.HistoryCollapsing
getNumComponents() - Method in class etomica.species.SpeciesSpheresCustom
getNumComponents() - Method in class etomica.species.SpeciesSpheresHetero
getNumConnections() - Method in class etomica.virial.cluster.ClusterDiagram: returns the number of active connections in the cluster.
getNumDataSinks() - Method in class etomica.data.DataDistributer
getNumDataSinks() - Method in class etomica.data.DataGroupSplitter
getNumDataSinks() - Method in class etomica.data.DataSplitter
getNumDataSinks() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getNumDataSinks() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
getNumDelete() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
getNumDigitColumns() - Method in class etomica.graphics.DisplayTable
getNumEquilibrationSubsteps() - Method in class etomica.thermointegration.IntegratorThermodynamic: Returns the number of steps equilibration steps performed at each thermodynamic state point before data collection begins.
getNumerator() - Method in interface etomica.graph.model.Coefficient
getNumerator() - Method in class etomica.graph.model.impl.CoefficientImpl
getNumFieldPoints() - Method in class etomica.graph.operations.Mul.MulParameters
getNumInsert() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
getNumLeafAtoms() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
getNumLeafAtoms() - Method in class etomica.AlkaneEH.SpeciesMethane
getNumLeafAtoms() - Method in class etomica.models.nitrogen.SpeciesN2
getNumLeafAtoms() - Method in class etomica.models.nitrogen.SpeciesN2B
getNumLeafAtoms() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
getNumLeafAtoms() - Method in class etomica.models.OPLS.SpeciesAceticAcid
getNumLeafAtoms() - Method in class etomica.models.rowley.SpeciesEthanol
getNumLeafAtoms() - Method in class etomica.models.rowley.SpeciesMethanol
getNumLeafAtoms() - Method in class etomica.models.traPPE.SpeciesMethanol
getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater3P
getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater3POriented
getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater4P
getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater4PCOM
getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater4POriented
getNumLeafAtoms() - Method in class etomica.normalmode.SpeciesHSDimer
getNumLeafAtoms() - Method in class etomica.paracetamol.SpeciesParacetamol
getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheres
getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheresCustom
getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheresHetero
getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheresMono
getNumLeafAtoms() - Method in class etomica.virial.Species7SiteRigidSF6
getNumLeafAtoms() - Method in class etomica.virial.SpeciesAlkaneEH
getNumLeafAtoms() - Method in class etomica.virial.SpeciesAnthracene3site464
getNumLeafAtoms() - Method in class etomica.virial.SpeciesAnthracene3site545
getNumLeafAtoms() - Method in class etomica.virial.SpeciesMethane
getNumLeafAtoms() - Method in class etomica.virial.SpeciesPh3site464
getNumLeafAtoms() - Method in class etomica.virial.SpeciesPh3site545
getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPEAnthracene
getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPECO2
getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPENaphthalene
getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
getNumMembraneLayers() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getNumMembraneLayers() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: Returns the number of membrane layers.
getNumNodes() - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
getNumNodes() - Method in class etomica.virial.cluster.ClusterTreeNode
getNumO2() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getNumRawData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getNumRootPoints() - Method in class etomica.virial.cluster.ClusterDiagram
getNumSubSteps() - Method in class etomica.overlap.IntegratorOverlap: Retruns the number of total number of integrator steps the sub-integrators perform for every step of the overlap integrator.
getNumSubsteps() - Method in class etomica.thermointegration.IntegratorThermodynamic: Returns the number of steps performed at each thermodynamic state point.
getNumSubSteps() - Method in class etomica.virial.overlap.IntegratorOverlap: Retruns the number of total number of integrator steps the sub-integrators perform for every step of the overlap integrator.
getNumSurfaceSites() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getNumSurfaceSites() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getNumTargets() - Method in class etomica.virial.overlap.DataVirialOverlap
getNumTrial() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
getNumTrial() - Method in class etomica.virial.MCMoveClusterRingRegrow
getNumTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
getNumUpdates() - Method in class etomica.nbr.list.NeighborListManager: Returns the number of times the neighbor lists have been updated.
getNumValues() - Method in class etomica.virial.ClusterSumIC
getNumXCells() - Method in class etomica.modules.sam.Sam
getNumZCells() - Method in class etomica.modules.sam.Sam
getNValues() - Method in class etomica.data.DataSourceUniform: Accessor method for number of values.
getObject() - Method in class etomica.modifier.ModifierGeneral
getObject(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
getOctant(Point3f) - Static method in class org.jmol.util.Quadric
getOelement() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
getOffDiagonalElements() - Method in class etomica.math.linearalgebra.EigenSystemReduction
getOffset() - Method in class etomica.modules.sam.P1Sinusoidal
getOldPartners() - Method in class etomica.potential.PotentialReactive.BondChangeData
getOmegaSquared() - Method in interface etomica.normalmode.NormalModes: Returns an array giving the frequencies (squared) corresponding to the normal-mode motions.
getOmegaSquared() - Method in class etomica.normalmode.NormalModes1DHR
getOmegaSquared() - Method in class etomica.normalmode.NormalModes2D
getOmegaSquared() - Method in class etomica.normalmode.NormalModes3D
getOmegaSquared() - Method in class etomica.normalmode.NormalModesFromFile
getOmegaSquared() - Method in class etomica.normalmode.NormalModesMolecular
getOmegaSquared() - Method in class etomica.normalmode.NormalModesPotential
getOmegaSquared() - Method in class etomica.normalmode.NormalModesSoftSpherical
getOmegaSquared() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getOneEValButtonsVisibility() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
getOneWVButtonsVisibility() - Method in class etomica.normalmode.DeviceWaveVectorSlider
getOperation() - Method in class etomica.graph.engine.impl.BinaryOpImpl
getOperation() - Method in class etomica.graph.engine.impl.UnaryOpImpl
getOperation() - Method in interface etomica.graph.engine.Parser.BinaryOp
getOperation() - Method in interface etomica.graph.engine.Parser.UnaryOp
getOptionDescription() - Method in interface etomica.graph.view.rasterizer.Main.OptionHandler: Returns the description for this option
getOptionValuesLength() - Method in class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
getOptionValuesLength() - Method in interface etomica.graph.view.rasterizer.Main.OptionHandler: Returns the number of values which the option handler requires.
getOptionValuesLength() - Method in class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
getOrderBeta() - Method in class etomica.virial.cluster.VirialDiagramsPT
getOrientation() - Method in class etomica.atom.AtomOriented
getOrientation() - Method in class etomica.atom.AtomOrientedDynamic
getOrientation() - Method in interface etomica.atom.IAtomOriented: Returns the orientation of the IAtom.
getOrientation() - Method in interface etomica.atom.IMoleculeOriented: Returns the orientation of the IAtom.
getOrientation() - Method in class etomica.atom.MoleculeOriented
getOrientation() - Method in class etomica.math.Quaternion: Returns an orientation corresponding to the rotation of cartesian coordinate frame {i,j,k} by the axis and angle associated with the Quaternion q.
getOrientationIndex(IVectorMutable) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
getOrientationIndex(IVectorMutable) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
getOrigin() - Method in class etomica.graphics.DisplayBox
getOrigin() - Method in class etomica.graphics.DisplayPolytope
getOrigin() - Method in class etomica.lattice.LatticePlane
getOtherAngles() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getOtherDensities() - Method in class etomica.normalmode.MeterDDP
getOtherDensities() - Method in class etomica.normalmode.MeterDP
getOtherTemperature() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getOtherTemperatures() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getOtherTemperatures() - Method in class etomica.normalmode.MeterTargetTP
getOType() - Method in class etomica.models.traPPE.SpeciesMethanol
getOType() - Method in class etomica.paracetamol.SpeciesParacetamol
getOut() - Method in class etomica.data.DataSinkConsole: Method called to express incredulity.
getOutDegree(byte) - Method in interface etomica.graph.model.Graph
getOutDegree(byte) - Method in class etomica.graph.model.impl.GraphImpl
getOutDegree() - Method in class etomica.virial.ClusterSumHS: Returns outDegee (number of bonds for each point) of the configuration passed to checkConfig
getOutDegree() - Method in interface etomica.virial.ClusterWheatley: Returns outDegee (number of bonds for each point) of the configuration passed to checkConfig
getOutDegree() - Method in class etomica.virial.ClusterWheatleyHS: Returns outDegee (number of bonds for each point) of the configuration passed to checkConfig
getOutDegree() - Method in class etomica.virial.ClusterWheatleyPartitionScreening: Returns outDegee (number of bonds for each point) of the configuration passed to checkConfig
getOutDegreeCore() - Method in class etomica.virial.ClusterWheatleyExtendSW
getOutDegreeWell() - Method in class etomica.virial.ClusterWheatleyExtendSW
getOuterGraph() - Method in class etomica.graph.iterators.CartesianIterator
getOuterIterator() - Method in class etomica.atom.iterator.ApiInnerVariable: Accessor method for the outer-loop atom iterator.
getOuterIterator() - Method in class etomica.atom.iterator.ApiIntergroup: Accessor method for the outer-loop atom iterator.
getOuterIterator() - Method in class etomica.atom.iterator.MpiInnerFixed: Accessor method for the outer-loop atom iterator.
getOuterIterator() - Method in class etomica.atom.iterator.MpiInnerVariable: Accessor method for the outer-loop atom iterator.
getOuterIterator() - Method in class etomica.graph.iterators.CartesianIterator
getOuterList() - Method in class etomica.atom.iterator.ApiInterArrayList: Returns the outer list used to generate the pairs.
getOuterList() - Method in class etomica.atom.iterator.MpiInterArrayList: Returns the outer list used to generate the pairs.
getOuterPermutation() - Method in class etomica.graph.iterators.CartesianPermutator
getOuterPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
getOuterRadius() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
getOutNode(byte, byte) - Method in interface etomica.graph.model.Graph
getOutNode(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
getOverlapAverage() - Method in class etomica.virial.overlap.DataVirialOverlap: Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to reference/target) for the optimal value of the Bennett parameter.
getOverlapAverage(int) - Method in class etomica.virial.overlap.DataVirialOverlap: Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to target/reference) for the given value of the Bennet parameter.
getOverlapAverageAndError() - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
getOverlapAverageAndError() - Method in class etomica.overlap.DataOverlap: Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to reference/target) for the optimal value of the Bennett parameter.
getOverlapAverageAndError() - Method in class etomica.virial.overlap.DataSourceVirialOverlap: Returns the ratio of the reference to target overlap-to-virial ratios (which reduces to reference/target) for the optimal value of the Bennett parameter.
getOverlapAverageAndErrorForAlpha(double) - Method in class etomica.virial.overlap.DataVirialOverlap: Returns the overlap average and uncertainty for a given value of alpha.
getOverlapAverageForAlpha(double) - Method in class etomica.virial.overlap.DataSourceVirialOverlap
getOxygenType() - Method in class etomica.models.rowley.SpeciesEthanol
getOxygenType() - Method in class etomica.models.rowley.SpeciesMethanol
getOxygenType() - Method in class etomica.models.water.SpeciesWater3P
getOxygenType() - Method in class etomica.models.water.SpeciesWater3POriented
getOxygenType() - Method in class etomica.models.water.SpeciesWater4P
getOxygenType() - Method in class etomica.models.water.SpeciesWater4PCOM
getOxygenType() - Method in class etomica.models.water.SpeciesWater4POriented
getOxygenType() - Method in class etomica.virial.SpeciesTraPPECO2
getP(int) - Method in class etomica.normalmode.MeterDDP
getP(int) - Method in class etomica.normalmode.MeterDP
getp1Counter() - Method in class etomica.normalmode.P1ConstraintNbrHcp
getPaddingSigma() - Method in class etomica.graphics.DisplayBox: Returns the amount of padding added around the edge of the drawing area.
getPaintAction(IBox) - Method in class etomica.graphics.SimulationGraphic: getPaintAction()
getPairAgent(IAtomType, IAtomType) - Method in class etomica.models.co2.PNGCPM
getPairAgent(IAtomType, IAtomType) - Method in class etomica.models.co2.PNGCPMX
getPairMoleculesIndex(IMolecule, IMolecule, boolean) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
getPairMoleculesIndex(IMolecule, IMolecule, boolean) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
getPairSiteValidation(String, IMolecularModel_SpeciesFactory[]) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
getPalette(String) - Static method in enum org.jmol.constant.EnumPalette
getPaletteID(String) - Static method in enum org.jmol.constant.EnumPalette
getPaletteName(byte) - Static method in enum org.jmol.constant.EnumPalette
getPanel() - Method in class etomica.graphics.DeviceSlider
getPanel() - Method in class etomica.graphics.DeviceSpinner
getPanel() - Method in class etomica.graphics.SimulationGraphic: A visual display of the simulation via a JPanel.
getPanel() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
getPanel() - Method in class etomica.modules.crystalviewer.LatticeEditor
getParallelAxis(IMolecule) - Method in class etomica.models.co2.PNGCPM.GCPMAgent
getParamAndValues() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getParameter(double) - Method in class etomica.models.nitrogen.BetaPhaseLatticeParameter
getParameter(double) - Method in class etomica.models.nitrogen.BetaPhaseLatticeParameterLS
getParameter(int) - Method in class etomica.models.nitrogen.BetaPhaseLatticeParameterNA
getParameterCount() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getParameters() - Static method in class etomica.modules.render.RenderMD
getParameters() - Static method in class etomica.simulation.prototypes.HSMD3D
getParametersArray() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getParameterValue(String) - Method in class etomica.graphics.DevicePlotPoints: Returns the value of the function parameter slider.
getParameterWrapper() - Method in class etomica.util.ParseArgs: Returns the parameter wrapper.
getParameterWrapper() - Method in class etomica.util.ReadParameters: Returns the parameter wrapper.
getParameterWrapper() - Method in class etomica.util.WriteParameters: Returns the parameter wrapper.
getParamType(int) - Static method in class org.jmol.script.Token
getParentGroup() - Method in interface etomica.api.IAtom: Returns the parent AtomGruop of this IAtom.
getParentGroup() - Method in class etomica.atom.Atom
getParentType() - Method in class etomica.atom.AtomTypeLeaf
getParsers() - Method in class etomica.util.ParameterBase
getPbcEnforcer() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getPbcEnforcer() - Method in class etomica.nbr.list.NeighborListManager
getPCenter(int) - Method in class etomica.normalmode.MeterDDP
getPCenter(int) - Method in class etomica.normalmode.MeterDP
getPcom() - Method in class etomica.util.numerical.Function1d
getPdbBondInfo(int) - Static method in class org.jmol.viewer.JmolConstants
getPendingActions() - Method in interface etomica.action.activity.ActivityGroup: Returns all actions from this group that have not yet started.
getPendingActions() - Method in class etomica.action.activity.ActivityGroupParallel
getPendingActions() - Method in class etomica.action.activity.ActivityGroupSeries
getPerimeter() - Method in class etomica.math.geometry.Cube: Returns 12*edgeLength
getPerimeter() - Method in class etomica.math.geometry.Cuboid
getPerimeter() - Method in class etomica.math.geometry.Parallelepiped
getPerimeter() - Method in class etomica.math.geometry.Parallelogram
getPerimeter() - Method in class etomica.math.geometry.Polygon: Returns the sum of the length of the edges of the polygon
getPerimeter() - Method in class etomica.math.geometry.Polyhedron: Returns the sum of the length of the edges of the polyhedron
getPerimeter() - Method in class etomica.math.geometry.Rectangle: Returns the perimeter of the rectangle.
getPeriodicity(int) - Method in interface etomica.api.IBoundary: Returns true if the boundary is periodic in the given direction (as defined by the getEdgeVector method).
getPeriodicity(int) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
getPeriodicity(int) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
getPeriodicity(int) - Method in class etomica.space.BoundaryDeformablePeriodic
getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularNonperiodic
getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularPeriodic
getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularPore
getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularSlit
getPeriodicity(int) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
getPerp(IVector, IVectorMutable, IVectorMutable) - Method in class etomica.models.co2.P2CO2H2OWheatley
getPerp(IVector, IVectorMutable, IVectorMutable) - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
getPerp(IVector, IVectorMutable, IVectorMutable) - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
getPerspectiveDepth() - Method in class g3dsys.control.G3DSys
getPhaseAngles() - Method in class etomica.normalmode.NormalModesVariable
getPhi() - Method in class etomica.potential.P4TorsionDreiding
getPhongExponent() - Static method in class org.jmol.util.GData
getPickedDiagram() - Method in class etomica.virial.cluster.ClusterDiagramTree
getPickedDiagram() - Method in interface etomica.virial.cluster.DiagramSource
getPixelDepth() - Method in class g3dsys.control.G3DSys: Gets the pixel depth of the display (zbuffer)
getPixelHeight() - Method in class g3dsys.control.G3DSys: Gets the pixel height of the display
getPixelUnit() - Method in class etomica.graphics.DisplayBox
getPixelUnit() - Method in class etomica.graphics.DisplayCanvas: Returns unit for conversion between simulation units and display pixels.
getPixelUnit() - Method in class etomica.graphics.DisplayPolytope: Returns unit for conversion between simulation units and display pixels.
getPixelUnitToMillimeter() - Method in class etomica.graph.view.rasterizer.SVGConverter
getPixelWidth() - Method in class g3dsys.control.G3DSys: Gets the pixel width of the display
getPlane() - Method in class etomica.lattice.LatticePlane
getPlaneColor() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Gets the color of the plane.
getPlaneProjection(Point3f, Point4f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
getPlaneThroughPoint(Point3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
getPlaneThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
getPlot() - Method in class etomica.graphics.DisplayPlot: Accessor method to plot class so that its properties can be edited.
getPlotSizeSlider(int) - Method in class etomica.graphics.DevicePlotPoints: Returns the plot scale slider for the given parameter (values can be DevicePlotPoints.MIN_X, MAX_X, MIN_Y or MAX_Y.
getPoint() - Method in class g3dsys.images.Ball
getPoint() - Method in class g3dsys.images.Ellipse
getPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNCO2GCPM: This returns the polarizable portion of the GCPM potential for any number of atoms.
getPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM: This returns the polarizable portion of the GCPM potential for any number of atoms.
getPolarizationEnergy(IMoleculeList) - Method in class etomica.models.water.PNWaterGCPM: This returns the polarizable portion of the GCPM potential for any number of atoms.
getPolarizationEnergy(IMoleculeList) - Method in interface etomica.potential.PotentialPolarizable: Returns the polarization contribution (non pairwise-additive) to the energy for the given AtomSet.
getPolytope() - Method in class etomica.graphics.DisplayPolytope
getPoreCenters() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
getPoreDim() - Method in class etomica.space.BoundaryRectangularPore: Returns index of periodic dimension.
getPoreRadius() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
getPos(int) - Method in class etomica.models.co2.P2CO2Hellmann
getPosition() - Method in interface etomica.api.IAtom: Returns the position of the IAtom.
getPosition() - Method in class etomica.atom.Atom
getPosition() - Method in interface etomica.atom.IMoleculePositioned: Returns the position of the IMolecule.
getPosition() - Method in class etomica.atom.MoleculeOriented
getPosition() - Method in class etomica.lattice.LatticePlane: Returns the position i, such the the plane is located at the i-th from the origin.
getPosition() - Method in class etomica.math.geometry.Hypersphere
getPosition() - Method in class etomica.math.geometry.Polytope: Returns the geometric center of the polytope.
getPositionDataInfo() - Method in interface etomica.data.DataSourcePositioned
getPositionDataInfo() - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
getPositionDefinition() - Method in class etomica.action.BoxImposePbc
getPositionDefinition() - Method in class etomica.atom.AtomFilterInShape
getPositionDefinition() - Method in class etomica.data.meter.MeterProfileByAtoms
getPositionDefinition() - Method in class etomica.data.meter.MeterProfileByVolume
getPositionDefinition() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
getPositionDefinition() - Method in class etomica.normalmode.CoordinateDefinitionMolecule
getPositionDefinition() - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
getPositionDefinition() - Method in class etomica.virial.CoordinatePairMoleculeSet
getPositionSource() - Method in class etomica.data.meter.MeterProfile: Returns the RandomPositionSource used by this meter.
getPositionSource() - Method in class etomica.data.meter.MeterWidomInsertion: Returns the RandomPositionSource used by this meter.
getPositionSource() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Returns the RandomPositionSource used by this move.
getPositionSource() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange: Returns the RandomPositionSource used by this move.
getPositionSource() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Returns the RandomPositionSource used by this meter.
getPositionSource() - Method in class etomica.liquidLJ.MeterWidomInsertionP: Returns the RandomPositionSource used by this meter.
getPositionSource() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
getPositivePrefix() - Method in class etomica.util.ScientificFormat
getPositiveSuffix() - Method in class etomica.util.ScientificFormat
getPostAction() - Method in class etomica.graphics.Device
getPotential(ISpecies[]) - Method in interface etomica.api.IPotentialMaster: Returns the potential that applies to the specified types, or null of no existing potential applies.
getPotential() - Method in class etomica.chem.models.Model.PotentialAndIterator
getPotential() - Method in class etomica.data.meter.MeterEnergy
getPotential(ISpecies[]) - Method in class etomica.potential.PotentialMaster
getPotential() - Method in class etomica.virial.ClusterSumIC.FR2
getPotential() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getPotential() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getPotential() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getPotential() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getPotential() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getPotential() - Method in class etomica.virial.MayerD2FDT2Spherical
getPotential() - Method in class etomica.virial.MayerDFDTSpherical
getPotential() - Method in class etomica.virial.MayerDFQFHDTSpherical
getPotential() - Method in class etomica.virial.MayerEGeneral
getPotential() - Method in class etomica.virial.MayerENonGeneral
getPotential() - Method in class etomica.virial.MayerESpherical
getPotential() - Method in interface etomica.virial.MayerFunction
getPotential() - Method in class etomica.virial.MayerFunctionProductGeneral
getPotential() - Method in class etomica.virial.MayerFunctionSum
getPotential() - Method in class etomica.virial.MayerFunctionSumGeneral
getPotential() - Method in class etomica.virial.MayerFunctionTemperature
getPotential() - Method in class etomica.virial.MayerGeneral
getPotential() - Method in class etomica.virial.MayerGeneralAtomic
getPotential() - Method in class etomica.virial.MayerGeneralSpherical
getPotential() - Method in class etomica.virial.MayerHardSphere
getPotential() - Method in class etomica.virial.MayerPTAtt
getPotential() - Method in class etomica.virial.MayerPUGeneral
getPotential() - Method in class etomica.virial.MayerSphericalPTAtt
getPotential() - Method in class etomica.virial.MayerSSSeries
getPotential() - Method in class etomica.virial.MayerWell
getPotential() - Method in class etomica.virial.MayerXSpherical
getPotential() - Method in class etomica.virial.MuFGeneral
getPotential() - Method in class etomica.virial.MuGeneral
getPotential1BodyList(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getPotential1BodyList(IAtom) - Method in class etomica.nbr.list.NeighborListManager
getPotentialCalculation() - Method in class etomica.mappedvirial.MeterMappedU
getPotentialCalculation() - Method in class etomica.mappedvirial.MeterMappedVirial
getPotentialCalculation() - Method in class etomica.mappedvirial.MeterMappedVirialV
getPotentialCalculations() - Method in interface etomica.threaded.IPotentialCalculationThreaded
getPotentialCalculations() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
getPotentialCollectionFactory() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
getPotentialEnergy() - Method in class etomica.data.meter.MeterEnergy
getPotentialEnergy() - Method in class etomica.integrator.IntegratorBox
getPotentialEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getPotentialGroupInterNonBondedLike() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getPotentialGroupInterNonBondedUnlike() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
getPotentialGroupIntraBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getPotentialIndex(IPotential) - Method in class etomica.potential.PotentialArray: Returns the index that this type has assigned to the given potential.
getPotentialIndex(IPotential) - Method in class etomica.potential.PotentialArrayByType: Returns the index that this type has assigned to the given potential.
getPotentialIndex(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular: Returns the index that this type has assigned to the given potential.
getPotentialIntraBondedTorsion() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getPotentialJList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialJList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialListDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialListDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialMaster() - Method in class etomica.integrator.IntegratorBox
getPotentialMaster() - Method in class etomica.modules.vle.MeterPressure2: Returns the integrator associated with this instance.
getPotentialMaster() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getPotentialMasterCell() - Method in class etomica.nbr.PotentialMasterHybrid
getPotentialMasterList() - Method in class etomica.nbr.PotentialMasterHybrid
getPotentialMolecularNonBondedLike() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
getPotentialMolecularUnlike() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
getPotentialParamAndValuesString() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getPotentialParamDispayTable() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialParamDispayTable() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialParamDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialParamDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialParamDisplayTM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialParamDisplayTM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialParamDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getPotentialParamDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getPotentialParamString() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getPotentialPlus() - Method in class etomica.virial.MayerSphericalPlus
getPotentialRange() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Returns the potential range.
getPotentialRange() - Method in class etomica.nbr.cell.NeighborCellManager: Returns the potential range.
getPotentials() - Method in interface etomica.api.IPotentialMaster: Returns an array containing all molecular Potentials.
getPotentials() - Method in class etomica.chem.models.Model: Returns an array of objects wrapping bonding Potentials and the AtomsetIteratorBasisDependents that return atoms appropriate for those potentials.
getPotentials() - Method in class etomica.chem.models.ModelChain
getPotentials() - Method in class etomica.potential.PotentialArray
getPotentials() - Method in class etomica.potential.PotentialArrayByType
getPotentials() - Method in class etomica.potential.PotentialArrayMolecular
getPotentials() - Method in class etomica.potential.PotentialGroup
getPotentials() - Method in class etomica.potential.PotentialMaster
getPotentials() - Method in class etomica.threaded.PotentialThreaded
getPotentialsClassList() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getPotentialsCollectionBuilder() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
getPotentialSiteAtIndex(int) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getPotentialSites() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getPotentialsList() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getPotentialsSelectedIndex() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getPreAction() - Method in class etomica.graphics.Device: Returns the action to be performed before the primary action executed by the device.
getPrecision() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
getPrecision() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
getPrecision() - Method in class etomica.graphics.DecimalSlider: Accessor method for precision of slider, defined as number of digits after the decimal that will be distinguished by slider.
getPrecision() - Method in class etomica.graphics.DeviceBox: Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() - Method in class etomica.graphics.DeviceSlider
getPrecision() - Method in class etomica.graphics.DeviceTernarySelector: Accessor method for the precision of the mole fractions.
getPrecision() - Method in class etomica.graphics.DisplayTable: Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() - Method in class etomica.graphics.DisplayTextBox: Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() - Method in class etomica.graphics.DisplayTextBoxesCAE: Accessor method of the precision, which specifies the number of significant figures to be displayed.
getPrecision() - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
getPrefix() - Method in class etomica.units.PrefixedUnit
getPressure() - Method in class etomica.association.MCMoveVolumeAssociated
getPressure() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
getPressure() - Method in class etomica.integrator.mcmove.MCMoveVolume
getPressure() - Method in class etomica.mappedvirial.MappedUpotential
getPressure() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
getPressure() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
getPressure() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
getPressure() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
getPressure() - Method in class etomica.normalmode.MCMoveVolumeSolid
getPressure() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
getPressure() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
getPressure() - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
getPressure() - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
getPressure(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
getPressure() - Method in class etomica.potential.P1HardMovingBoundary
getPressure1() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
getPressure1XYZ() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
getPressureDimension() - Method in class etomica.association.MCMoveVolumeAssociated
getPressureDimension() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
getPressureDimension() - Method in class etomica.integrator.mcmove.MCMoveVolume
getPressureDimension() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
getPressureDimension() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
getPressureDimension() - Method in class etomica.normalmode.MCMoveVolumeSolid
getPressureDimension() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
getPressureDimension() - Method in class etomica.potential.P1HardMovingBoundary
getPressureSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
getPressureSumXYZ() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
getPressureTensor() - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB: Returns the virial portion of pressure tensor calculated during the last potential calculation.
getPressureTensor() - Method in class etomica.integrator.IntegratorRigidIterative: Returns the pressure tensor based on the forces calculated during the last time step.
getPressureTensor() - Method in class etomica.integrator.IntegratorRigidMatrixIterative: Returns the pressure tensor based on the forces calculated during the last time step.
getPressureTensor() - Method in class etomica.integrator.IntegratorVelocityVerlet: Returns the pressure tensor based on the forces calculated during the last time step.
getPressureTensor() - Method in class etomica.integrator.IntegratorVerlet: Returns the pressure tensor based on the forces calculated during the last time step.
getPressureTensor() - Method in class etomica.modules.droplet.IntegratorDroplet: Returns the pressure tensor based on the forces calculated during the last time step.
getPressureTensor() - Method in class etomica.potential.PotentialCalculationForcePressureSum: Returns the virial portion of pressure tensor calculated during the last potential calculation.
getPressureTensor() - Method in class etomica.potential.PotentialCalculationPressureTensor: Returns the pressure tensor based on a previous call to PotentialMaster.calculate
getPressureTensor() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion: Returns the pressure tensor based on the forces calculated during the last time step.
getPrevX() - Method in class etomica.graphics.DisplayCanvas
getPrevY() - Method in class etomica.graphics.DisplayCanvas
getPrimitive() - Method in class etomica.lattice.BravaisLattice: Returns the primitive object used to construct this lattice.
getPrimitive() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
getPrimitive() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
getPrimitive() - Method in class etomica.normalmode.CoordinateDefinition
getPrimitiveFcc() - Method in class etomica.lattice.LatticeCubicFcc: Returns a new PrimitiveFcc instance corresponding to the fcc lattice.
getPrimitiveHexagonal() - Method in class etomica.lattice.LatticeOrthorhombicHexagonal: Returns a new PrimitiveFcc instance corresponding to the fcc lattice.
getPriority() - Method in class etomica.action.BoxImposePbc
getPriority() - Method in class etomica.zeolite.MSDCoordWriter
getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
getProductOfFrequencies() - Method in class etomica.action.CalcVibrationalModes
getProfileDataInfo() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
getProfileDim() - Method in class etomica.data.meter.MeterProfile: Accessor method for vector describing the direction along which the profile is measured.
getProfileDim() - Method in class etomica.data.meter.MeterProfileByAtoms: Accessor method for vector describing the direction along which the profile is measured.
getProfileDim() - Method in class etomica.data.meter.MeterProfileByVolume: Accessor method for vector describing the direction along which the profile is measured.
getProfileDim() - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
getPrompt() - Method in class etomica.graph.engine.ConsoleUI
getProperty() - Method in class etomica.graph.engine.impl.CommandPropertyValueImpl
getProperty() - Method in interface etomica.graph.engine.Parser.CommandPropertyValue
getProperty() - Method in class etomica.graphics.DeviceSlider
getProperty() - Method in class etomica.graphics.DeviceSpinner
getProperty() - Method in class etomica.modifier.ModifierGeneral
getPropertyNames() - Method in interface etomica.graph.engine.Environment
getPropertyNames() - Method in class etomica.graph.engine.impl.EnvironmentImpl
getPropertyValue(String) - Method in interface etomica.graph.engine.Environment
getPropertyValue(String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
getPType() - Method in class etomica.models.nitrogen.SpeciesN2
getPType() - Method in class etomica.models.nitrogen.SpeciesN2B
getPType() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
getPushInterval() - Method in class etomica.data.DataAccumulator: Accumulated data are pushed to the data sinks after every pushInterval calls to putData.
getPYCorrection(byte) - Static method in class etomica.virial.PYGenerator: Returns graphs included in the correction to the PY approximation at the n-th order.
getQ() - Method in class etomica.chem.electrostatics.Charge
getQ() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
getQ() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
getQ(int) - Method in class etomica.models.co2.P2CO2Hellmann
getQ() - Static method in class etomica.models.water.P2WaterSzalewicz
getQ0() - Method in class etomica.math.Quaternion: Returns the q0 component of the Quaternion
getQ1() - Method in class etomica.math.Quaternion: Returns the q1 component of the Quaternion
getQ2() - Method in class etomica.math.Quaternion: Returns the q2 component of the Quaternion
getQ3() - Method in class etomica.math.Quaternion: Returns the q3 component of the Quaternion
getqp() - Method in class etomica.mappedvirial.MappedUpotential
getQP_Q() - Method in class etomica.mappedvirial.MappedUpotential
getQU() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
getQU() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
getQuadrupolarMomentSquare() - Method in class etomica.potential.P2LJQ
getQuadrupolarMomentSquare() - Method in class etomica.potential.P2LJQQ
getQuality() - Method in class etomica.graph.view.rasterizer.SVGConverter
getQuardricZ(double, double, double[], double[]) - Static method in class org.jmol.util.Quadric
getQuaternion() - Method in class etomica.atom.AtomOrientedQuaternion
getQuaternionFrame(Point3f, Tuple3f, Tuple3f) - Static method in class org.jmol.util.Quaternion
getQuaternionFrameV(Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Quaternion
getQuotedAttribute(String, String) - Static method in class org.jmol.util.Parser
getQuotedStringAt(String, int) - Static method in class org.jmol.util.Parser
getQuotedStringNext(String, int[]) - Static method in class org.jmol.util.Parser
getR0() - Method in class etomica.potential.P2Harmonic: Separation at which potential is at its minimum.
getR0Dimension() - Method in class etomica.potential.P2Harmonic
getr2(int, int) - Method in class etomica.virial.CoordinatePairLeafSet: Returns atom pair for ith and jth atoms in set.
getr2(int, int) - Method in class etomica.virial.CoordinatePairMoleculeSet: Returns atom pair for ith and jth atoms in set.
getr2(int, int) - Method in interface etomica.virial.CoordinatePairSet: Returns atom pair for ith and jth atoms in set.
getR2Cut() - Method in class etomica.data.meter.MeterBondOrderParameterQ
getr2d2udr2(int, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
getRadius() - Method in class etomica.math.geometry.Hypersphere
getRadius() - Method in class etomica.potential.P1SoftBoundary: Returns the radius.
getRadius(int) - Static method in class org.jmol.util.Quadric
getRadiusDimension() - Method in class etomica.potential.P1SoftBoundary
getRandom() - Method in interface etomica.api.ISimulation: Returns the Simulation's random number generator.
getRandom() - Method in class etomica.simulation.Simulation
getRandomNumberGenerator() - Method in class etomica.association.AtomSourceRandomDimer: Returns the random number generator used to pick atoms
getRandomNumberGenerator() - Method in class etomica.association.AtomSourceRandomSmer: Returns the random number generator used to pick atoms
getRandomNumberGenerator() - Method in class etomica.association.MoleculeSourceRandomDimer: Returns the random number generator used to pick atoms
getRandomNumberGenerator() - Method in class etomica.atom.AtomSourceRandomLeaf: Returns the random number generator used to pick atoms
getRandomNumberGenerator() - Method in class etomica.atom.AtomSourceRandomSpecies: Returns the random number generator used to pick atoms
getRandomNumberGenerator() - Method in class etomica.atom.MoleculeSourceRandomMolecule: Returns the random number generator used to pick molecules
getRandomSeeds() - Method in class etomica.simulation.Simulation: Returns the seeds that were used for the random number generator at construction.
getRandSeedArray() - Static method in class etomica.util.RandomNumberGeneratorUnix: Convenience method that returns an array of integers, useful as seeds to another RNG.
getRange() - Method in interface etomica.api.IPotential: Returns the range over which the potential applies.
getRange() - Method in class etomica.freeenergy.npath.P1ImageHarmonic
getRange() - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare: Returns (a copy of) the array specifying the neighbor range.
getRange() - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti: Returns infinity.
getRange() - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat: Returns infinity.
getRange() - Method in class etomica.meam.PotentialCuLREP
getRange() - Method in class etomica.meam.PotentialEFS
getRange() - Method in class etomica.meam.PotentialFeEAM
getRange() - Method in class etomica.meam.PotentialFeEAM_LS
getRange() - Method in class etomica.meam.PotentialMEAM
getRange() - Method in class etomica.models.co2.P2CO2H2OWheatley
getRange() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
getRange() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
getRange() - Method in class etomica.models.co2.P2CO2Hellmann
getRange() - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
getRange() - Method in class etomica.models.co2.PNCO2GCPM
getRange() - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
getRange() - Method in class etomica.models.co2.PNGCPM
getRange() - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
getRange() - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
getRange() - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
getRange() - Method in class etomica.models.nitrogen.P2Nitrogen
getRange() - Method in class etomica.models.nitrogen.P2NitrogenAB
getRange() - Method in class etomica.models.nitrogen.P2NitrogenAnisotropic
getRange() - Method in class etomica.models.nitrogen.P2NitrogenShellModel
getRange() - Method in class etomica.models.nitrogen.PRotConstraint
getRange() - Method in class etomica.models.water.P2Water3P
getRange() - Method in class etomica.models.water.P2Water3PSoft
getRange() - Method in class etomica.models.water.P2Water4P
getRange() - Method in class etomica.models.water.P2Water4PSoft
getRange() - Method in class etomica.models.water.P2WaterSzalewicz
getRange() - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
getRange() - Method in class etomica.models.water.P2WaterTIP4P
getRange() - Method in class etomica.models.water.P2WaterTIP4PHardCore
getRange() - Method in class etomica.models.water.PNWaterGCPM
getRange() - Method in class etomica.modules.adsorption.P1Wall
getRange() - Method in class etomica.modules.catalysis.P2SquareWellBonding
getRange() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
getRange() - Method in class etomica.modules.catalysis.P2SquareWellSurface
getRange() - Method in class etomica.modules.colloid.P1Wall
getRange() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
getRange() - Method in class etomica.modules.dcvgcmd.P1WCAWall
getRange() - Method in class etomica.modules.droplet.P1Smash
getRange() - Method in class etomica.modules.droplet.P2Cohesion
getRange() - Method in class etomica.modules.materialfracture.P1Tension
getRange() - Method in class etomica.modules.mu.P2SquareWellOneSide
getRange() - Method in class etomica.modules.sam.P1Sinusoidal
getRange() - Method in class etomica.modules.sam.P1WCAWall
getRange() - Method in class etomica.nbr.cell.PotentialMasterCell
getRange() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getRange() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Returns the range that determines how far to look for neighbors.
getRange() - Method in class etomica.nbr.list.NeighborListManager
getRange() - Method in class etomica.nbr.list.PotentialMasterList: Returns the range that determines how far to look for neighbors.
getRange() - Method in class etomica.nbr.PotentialMasterHybrid
getRange() - Method in class etomica.normalmode.P1ConstraintNbr
getRange() - Method in class etomica.normalmode.P1ConstraintNbrHcp
getRange() - Method in class etomica.normalmode.P2XOrder: Returns infinity.
getRange() - Method in class etomica.potential.EwaldSummation
getRange() - Method in class etomica.potential.EwaldSummation.P2EwaldReal
getRange() - Method in class etomica.potential.EwaldSumMolecules
getRange() - Method in class etomica.potential.P1ExternalField
getRange() - Method in class etomica.potential.P1HardBoundary
getRange() - Method in class etomica.potential.P1HydrogenMielke
getRange() - Method in class etomica.potential.P22CLJQ
getRange() - Method in class etomica.potential.P2CO2EMP
getRange() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
getRange() - Method in class etomica.potential.P2DLPOLY
getRange() - Method in class etomica.potential.P2DoubleWell
getRange() - Method in class etomica.potential.P2EffectiveFeynmanHibbs
getRange() - Method in class etomica.potential.P2HardAssociation: Returns the well diameter.
getRange() - Method in class etomica.potential.P2HardAssociationCone: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeFourSites: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeOneSite: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeReference: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites: Returns infinity.
getRange() - Method in class etomica.potential.P2HardAssociationConeSW: Returns sigma * cutoffFactor.
getRange() - Method in class etomica.potential.P2HardBond: Returns infinity.
getRange() - Method in class etomica.potential.P2HardBondedList
getRange() - Method in class etomica.potential.P2HardSphere
getRange() - Method in class etomica.potential.P2HardWrapper
getRange() - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
getRange() - Method in class etomica.potential.P2HePCKLJS.P2HeTI
getRange() - Method in class etomica.potential.P2HeSimplified.P2HeQFH
getRange() - Method in class etomica.potential.P2HeSimplified.P2HeTI
getRange() - Method in class etomica.potential.P2HSDipole
getRange() - Method in class etomica.potential.P2HydrogenHinde
getRange() - Method in class etomica.potential.P2HydrogenHindeAtomic
getRange() - Method in class etomica.potential.P2HydrogenHindePatkowski
getRange() - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
getRange() - Method in class etomica.potential.P2HydrogenPatkowski
getRange() - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
getRange() - Method in class etomica.potential.P2Ideal: Returns zero.
getRange() - Method in class etomica.potential.P2LJDipole
getRange() - Method in class etomica.potential.P2LJQ
getRange() - Method in class etomica.potential.P2MoleculeMonatomic
getRange() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched: Returns the truncation radius.
getRange() - Method in class etomica.potential.P2MoleculeTruncated: Returns the truncation radius.
getRange() - Method in class etomica.potential.P2NitrogenHellmann
getRange() - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
getRange() - Method in class etomica.potential.P2O2Bartolomei
getRange() - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
getRange() - Method in class etomica.potential.P2PenetrableBond: Returns infinity.
getRange() - Method in class etomica.potential.P2PenetrableSphere
getRange() - Method in class etomica.potential.P2PenetrableSquareWell
getRange() - Method in class etomica.potential.P2QChem
getRange() - Method in class etomica.potential.P2ReactionFieldDipole
getRange() - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
getRange() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
getRange() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
getRange() - Method in class etomica.potential.P2SemiclassicalAtomic
getRange() - Method in class etomica.potential.P2SemiclassicalMolecular
getRange() - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the truncation radius.
getRange() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched: Returns the truncation radius.
getRange() - Method in class etomica.potential.P2SoftTruncated: Returns the truncation radius.
getRange() - Method in class etomica.potential.P2SpheroPolyhedron
getRange() - Method in class etomica.potential.P2SquareWell
getRange() - Method in class etomica.potential.P2SquareWellRobust
getRange() - Method in class etomica.potential.P2Tether: Returns the tether length.
getRange() - Method in class etomica.potential.P2TriangleWell
getRange() - Method in class etomica.potential.P2WaterPotentialsJankowski
getRange() - Method in class etomica.potential.P2WCA: Returns the range of the potential, which is the point of truncation.
getRange() - Method in class etomica.potential.P3AxilrodTeller
getRange() - Method in class etomica.potential.P3BondAngle
getRange() - Method in class etomica.potential.P3BondAngleDreiding
getRange() - Method in class etomica.potential.P3CPSNonAdditiveHe
getRange() - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
getRange() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
getRange() - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
getRange() - Method in class etomica.potential.P3HydrogenATM
getRange() - Method in class etomica.potential.P3HydrogenManzhos
getRange() - Method in class etomica.potential.P3Induction
getRange() - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
getRange() - Method in class etomica.potential.P4BondTorsion
getRange() - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
getRange() - Method in class etomica.potential.P4TorsionDreiding
getRange() - Method in class etomica.potential.Potential
getRange() - Method in class etomica.potential.Potential0: Returns zero.
getRange() - Method in class etomica.potential.Potential1: Returns zero.
getRange() - Method in class etomica.potential.Potential2SoftSpherical: Returns infinity.
getRange() - Method in class etomica.potential.Potential2SoftSphericalLS: Returns infinity.
getRange() - Method in class etomica.potential.PotentialAtomicSum
getRange() - Method in class etomica.potential.PotentialDLPOLY
getRange() - Method in class etomica.potential.PotentialEmul
getRange() - Method in class etomica.potential.PotentialGroup: Returns the maximum of the range of all potentials in the group.
getRange() - Method in class etomica.potential.PotentialMolecular
getRange() - Method in class etomica.potential.PotentialMolecularMonatomic
getRange() - Method in class etomica.potential.PotentialMolecularSum
getRange() - Method in class etomica.rotation.P2LJDipole
getRange() - Method in class etomica.spin.P2Spin: Returns 0, becuase potential operates on a lattice and range should not be needed.
getRange() - Method in class etomica.threaded.PotentialThreaded
getRange() - Method in class etomica.virial.P1IntraLambda
getRange() - Method in class etomica.virial.PotentialCommonAtomic
getRange() - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
getRange() - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
getRange() - Method in class etomica.virial.PotentialNonAdditive
getRange() - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
getRange() - Method in class etomica.yukawa.P2HC2Yukawa
getRangedPotentials(ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
getRangedPotentials(IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
getRatios() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener: Returns overlap sampling results (ratio of partition functions between sequential number of atoms).
getRawData() - Method in class etomica.data.AccumulatorAverageBlockless
getRawData() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
getRawData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getRawDataBlockSize() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getRawLogAccumulator() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getRawLogDataCorrelation() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Returns the correlation between consecutive values of the log of the "raw" data held by the accumulator.
getRCut() - Method in class etomica.potential.EwaldSummation: Returns real-space cutoff
getrdfdr(int, double, double) - Static method in class etomica.virial.BnHNCLJ
getrdfdr(int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnIETP2Spherical
getrdfdr(int, double, double) - Static method in class etomica.virial.BnPYLJ
getrdfdr(int, double, double) - Static method in class etomica.virial.BnSCALJ
getrdudr(int, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
getRe() - Method in class etomica.potential.P2ModifiedMorse
getRe() - Method in class etomica.potential.P2Morse
getReal() - Method in class etomica.util.FastFourierTransform: array value calls
getRealEigenvalues() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition: Return the real parts of the eigenvalues
getRealEigenvalues() - Method in class org.jmol.util.Eigen: Return the real parts of the eigenvalues
getReferenceDataInterval() - Method in class etomica.normalmode.SimOverlapModule
getRefPref() - Method in class etomica.normalmode.MeterSamplingHarmonic
getRefPref() - Method in class etomica.normalmode.MeterSamplingTarget
getRefPref() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
getRefPref() - Method in class etomica.normalmode.MeterWorkBennetTarget
getRefPref() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
getRefPref() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
getRefPref() - Method in class etomica.normalmode.MeterWorkTargetBennet
getRefPref() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
getRefPref() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
getRefPref() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
getRefPref() - Method in class etomica.normalmode.SimBennet
getRefPref() - Method in class etomica.normalmode.SimHarmonicUmbrella
getRefPref() - Method in class etomica.normalmode.SimTargetUmbrella
getRefPref() - Method in class etomica.normalmode.SimUmbrella
getRefPref() - Method in class etomica.normalmode.SimUmbrellaSoftSphere
getRefSource() - Method in class etomica.overlap.DataOverlap: Returns object capable of retrieving data from the reference system.
getRefStepFraction() - Method in class etomica.overlap.IntegratorOverlap
getRefTimeFraction() - Method in class etomica.overlap.IntegratorOverlap
getReinitButton() - Method in class etomica.graphics.DeviceTrioControllerButton
getRelaxationRateH() - Method in class etomica.integrator.IntegratorGear4NPH
getRelaxationRateHDimension() - Method in class etomica.integrator.IntegratorGear4NPH
getRelaxationRateP() - Method in class etomica.integrator.IntegratorGear4NPH
getRelaxationRatePDimension() - Method in class etomica.integrator.IntegratorGear4NPH
getRemove() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getRemoveSpecies1() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getRemoveSpecies2() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getRemoveSpecies3() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getRenderHeight() - Method in class org.jmol.util.GData: gets g3d height
getRenderWidth() - Method in class org.jmol.util.GData: gets g3d width
getReservoirSize() - Method in class etomica.atom.AtomLeafAgentManager
getReservoirSize() - Method in class etomica.atom.MoleculeAgentManager
getReset() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getReset() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getResetAction() - Method in class etomica.graphics.DeviceNSelector: Returns the action used to "reset" the simulation after changing the number of molecules, SimulationRestart by default.
getResetAveragesButton() - Method in class etomica.graphics.DeviceTrioControllerButton
getResizeOnNewBox() - Method in class etomica.graphics.DisplayBox: Get the flag indicating whether the graphic should resize from its currently displayed size when a new box is set.
getResults(Potential2SoftSpherical, double, double, double, boolean) - Static method in class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
getReverseEdgeColor(char) - Static method in class etomica.graph.model.impl.MetadataImpl
getRm() - Method in class etomica.potential.P2Exp6Buckingham
getRmax() - Method in class etomica.potential.P2Exp6Buckingham
getRmsd(Point3f[][], Quaternion) - Static method in class org.jmol.util.Measure
getRmSquared() - Method in class etomica.potential.P2Exp6Buckingham
getRootColorMap() - Method in class etomica.graph.engine.impl.ConstructorColoredImpl
getRootColorMap() - Method in interface etomica.graph.engine.Parser.ConstructorColored
getRootNodes() - Method in class etomica.graph.engine.impl.ConstructorMonoImpl
getRootNodes() - Method in interface etomica.graph.engine.Parser.ConstructorMono
getRotationAxis() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
getRotationMatrix() - Method in class etomica.math.Quaternion: Returns the rotation matrix associated with the Quaternion q as a Jama.Matrix
getRotationScale(Matrix3f) - Method in class org.jmol.util.Matrix4f: Gets the upper 3x3 values of this matrix and places them into the matrix m1.
getRow(int, float[]) - Method in class org.jmol.util.Matrix3f: Copies the matrix values in the specified row into the array parameter.
getRow(int, float[]) - Method in class org.jmol.util.Matrix4f: Copies the matrix values in the specified row into the array parameter.
getRowCount() - Method in class etomica.data.DataSinkTable: Returns the length of the longest column.
getRowCount() - Method in class etomica.graphics.DeviceTableModelGeneric: Get the number of rows in the table (including blank rows).
getRowCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
getRowCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
getRowCount() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
getRowHeader(int) - Method in class etomica.data.DataSinkTable
getRowHeader(int) - Method in class etomica.data.types.DataTable.DataInfoTable: Returns the row header for row i or an empty string if there are no row headers.
getRowHeaders() - Method in class etomica.data.types.DataTable.DataInfoTableFactory: Returns a copy of the row headers or null if no row headers exist.
getRowLabelColumnHeader() - Method in class etomica.graphics.DisplayTable: Returns the header of the row-label column.
getRowLabels() - Method in class etomica.graphics.DisplayTable: Descriptive text for each row.
getRPow() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
getRun() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getRun() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getSafetyFactor() - Method in class etomica.nbr.CriterionPositionWall: returns the safety factor
getSafetyFactor() - Method in class etomica.nbr.CriterionSimple
getSafetyFactor() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Returns the safety factor.
getSafetyFactor() - Method in class etomica.nbr.list.PotentialMasterList: Returns the safety factor.
getSafetyFactor() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
getSampleCluster() - Method in class etomica.virial.BoxCluster: returns the cluster used for sampling in this box
getSampleClusters() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
getSampleCount() - Method in class etomica.data.AccumulatorAverage
getSampleCount() - Method in class etomica.data.AccumulatorAverageBlockless
getSampleCount() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
getSampleCount() - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapAvg
getSampleCount() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
getSampleCount() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
getSampleCount() - Method in interface etomica.util.History: Returns the number of data samples currently held by the History.
getSampleCount() - Method in class etomica.util.HistoryCollapsing
getSampleCount() - Method in class etomica.util.HistoryComplete
getSampleCount() - Method in class etomica.util.HistoryScrolling
getSampleLogVariance() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getSampleVariance() - Method in class etomica.data.AccumulatorAverageCollapsingLog
getSaveValues() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
getSaveValues() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getSBOType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
getScalar() - Method in class etomica.math.Quaternion: Returns the scalar part of the Quaternion
getScalarEnergy() - Method in class etomica.conjugategradient.DerivativeEnergyFunction
getScale() - Method in class etomica.action.BoxInflate
getScale() - Method in class etomica.graphics.DisplayBox
getScale() - Method in class etomica.graphics.DisplayPolytope
getScaledCoordinates() - Method in class etomica.lattice.crystal.Basis: Returns scaled coordinates
getScaling() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
getScaling() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
getScalingDataSource() - Method in class etomica.data.meter.MeterPressureByVolumeChange: Returns the data source for volume scalings.
getScreenImage() - Method in class org.jmol.g3d.Graphics3D
getScreenImage() - Method in class org.jmol.util.GData
getSecondaryDirection() - Method in interface etomica.space3d.IOrientationFull3D: Returns a unit vector pointing in the orientation's secondary direction.
getSecondaryDirection() - Method in class etomica.space3d.OrientationFull3D
getSecondVector() - Method in class etomica.config.ConformationChainZigZag
getSecondVector() - Method in class etomica.config.ConformationChainZigZag2
getSecurityOff() - Method in class etomica.graph.view.rasterizer.SVGConverter: Returns whether or not scripts will be run securely
getSeed() - Method in class etomica.util.RandomMersenneTwister
getSeedArray() - Method in class etomica.util.RandomMersenneTwister
getSeen() - Method in class etomica.graph.traversal.AbstractTraversal
getSegments() - Method in class etomica.graph.property.FFTDecomposition
getSelectedMove() - Method in class etomica.integrator.mcmove.MCMoveManager
getSelectedRows() - Method in class etomica.graphics.DeviceTable: Returns the indices of all the selected rows on the table.
getSelectedSpecies() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSelector() - Method in class etomica.graphics.DeviceSelector
getSelector() - Method in class etomica.graphics.DeviceThermoSelector
getSet(GraphIterator) - Method in class etomica.graph.iterators.IteratorToSet
getSettableTokFromString(String) - Static method in class org.jmol.script.Token
getSgima() - Method in class etomica.potential.P1HardPeriodic
getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
getShadeIndex(float, float, float) - Static method in class org.jmol.util.Shader
getShadeIndexNormalized(float, float, float) - Static method in class org.jmol.util.Shader
getShades(short) - Static method in class org.jmol.util.Colix
getShades(short) - Method in class org.jmol.util.GData
getShades(int, boolean) - Static method in class org.jmol.util.Shader
getShadesArgb(int, boolean) - Static method in class org.jmol.util.Colix
getShadesGreyscale(short) - Static method in class org.jmol.util.Colix
getShakeAgentManager() - Method in class etomica.integrator.IntegratorVelocityVerletShake
getShakeTolerance() - Method in class etomica.integrator.IntegratorVelocityVerletShake
getShape() - Method in class etomica.atom.AtomFilterInShape
getShape() - Method in class etomica.data.meter.MeterLocalDensity
getShape() - Method in class etomica.data.meter.MeterLocalMoleFraction: Returns the subvolume shape for the mole fraction calculation.
getShape() - Method in class etomica.graphics.DeviceTrioControllerButton
getShape() - Method in class etomica.space.Boundary
getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JmolConstants
getShapeOrigin() - Method in class etomica.data.meter.MeterLocalMoleFraction: Returns the origin of the subvolume.
getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JmolConstants
getShearRate() - Method in class etomica.modules.rheology.IntegratorPolymer
getShearRateNumber() - Method in class etomica.modules.rheology.IntegratorPolymer
getShift() - Method in class etomica.interfacial.ConfigurationLammps
getShifts(IBoundary, IVector, double) - Method in class etomica.graphics.OverflowShift: Provides information needed so that drawing can be done of portions of the periodic images of an atom that overflow into the volume (because the periodic image is just outside the volume).
getShiftX() - Method in class etomica.graphics.DisplayCanvas
getShiftY() - Method in class etomica.graphics.DisplayCanvas
getShowBoundary() - Method in class etomica.graphics.DisplayBox: Get the flag indicating if the boundary should be drawn.
getShowSlider() - Method in class etomica.graphics.DeviceSlider
getShowValues() - Method in class etomica.graphics.DeviceSlider
getSideLength() - Method in class etomica.graphics.DeviceTernarySelector: Accessor method for the length of each side of the triangle, in pixels.
getSigma() - Method in class etomica.models.water.P2Water3P
getSigma() - Method in class etomica.models.water.P2Water3PSoft
getSigma() - Method in class etomica.models.water.P2Water4P
getSigma() - Method in class etomica.models.water.P2Water4PSoft
getSigma() - Method in class etomica.models.water.P2WaterTIP4P
getSigma() - Method in class etomica.models.water.P2WaterTIP4PHardCore
getSigma() - Method in class etomica.modules.adsorption.P1Wall
getSigma() - Method in class etomica.modules.colloid.P1Wall
getSigma() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall: Returns the radius.
getSigma() - Method in class etomica.modules.dcvgcmd.P1WCAWall: Returns the radius.
getSigma() - Method in class etomica.modules.sam.P1WCAWall: Returns the radius.
getSigma() - Method in class etomica.modules.vle.VLESim
getSigma() - Method in class etomica.potential.P22CLJQ
getSigma() - Method in class etomica.potential.P2HardAssociationCone: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeReference: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for Lennard-Jones size parameter
getSigma() - Method in class etomica.potential.P2HSDipole
getSigma() - Method in class etomica.potential.P2LennardJones: Accessor method for Lennard-Jones size parameter.
getSigma() - Method in class etomica.potential.P2LennardJonesDreiding: Accessor method for Lennard-Jones size parameter.
getSigma() - Method in class etomica.potential.P2LJDipole
getSigma() - Method in class etomica.potential.P2LJQ
getSigma() - Method in class etomica.potential.P2LJQQ
getSigma() - Method in class etomica.potential.P2SoftSphere: Accessor method for soft-sphere size parameter.
getSigma() - Method in class etomica.potential.P2WCA: Accessor method for the size parameter.
getSigma() - Method in class etomica.rotation.P2LJDipole
getSigma() - Method in class etomica.units.systems.LJ
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getSigma() - Method in class etomica.virial.MayerEHardSphere: Returns the HS diameter.
getSigma() - Method in class etomica.virial.MayerHardSphere: Returns the HS diameter.
getSigma() - Method in class etomica.yukawa.P2HC2Yukawa: Accessor methods for size and energy parameters.
getSigmaC() - Method in class etomica.potential.P2CO2EMP
getSigmaCO() - Method in class etomica.potential.P2CO2EMP
getSigmaColloid() - Method in class etomica.modules.colloid.ConfigurationColloid
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationCone
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeReference
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeReferenceFourSites
getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
getSigmaDimension() - Method in class etomica.potential.P2LennardJones
getSigmaDimension() - Method in class etomica.potential.P2LennardJonesDreiding
getSigmaDimension() - Method in class etomica.potential.P2ModifiedMorse
getSigmaDimension() - Method in class etomica.potential.P2Morse
getSigmaDimension() - Method in class etomica.potential.P2SoftSphere
getSigmaDimension() - Method in class etomica.potential.P2WCA
getSigmaHSRef(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getSigmaHSRefField(int) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getSigmaHSRefFieldA() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getSigmaHSRefFieldB() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getSigmaHSRefFieldC() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getSigmaHSRefSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getSigmaMonomer() - Method in class etomica.modules.colloid.ConfigurationColloid
getSigmaO() - Method in class etomica.potential.P2CO2EMP
getSignature(Graph) - Method in class etomica.graph.iterators.filters.GlobalFilter.SignatureMaker
getSignature() - Method in interface etomica.graph.model.Graph
getSignature() - Method in class etomica.graph.model.impl.GraphImpl
getSimEnvController() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
getSimRestart() - Method in class etomica.graphics.DeviceTrioControllerButton
getSimulation() - Method in interface etomica.action.SimulationAction
getSimulation() - Method in class etomica.action.SimulationActionAdapter
getSimulation() - Method in interface etomica.api.ISimulationEvent
getSimulation() - Method in class etomica.graphics.DeviceTrioControllerButton: Returns the simulation affected by the buttons.
getSimulation() - Method in class etomica.graphics.SimulationGraphic
getSimulation() - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular: Returns the simulation associated with this PotentialMaster
getSimulation() - Method in class etomica.nbr.PotentialMasterNbr: Returns the simulation associated with this PotentialMaster
getSimulation() - Method in interface etomica.simulation.SimulationContainer
getSimulation() - Method in class etomica.simulation.SimulationEvent
getSite(IAtom) - Method in class etomica.nbr.site.NeighborSiteManager
getSite() - Method in enum etomica.virial.GUI.models.EnumSiteName
getSiteDisplacementIndex() - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
getSiteDisplacementIndex(IVectorMutable) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
getSiteFactor() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
getSiteManager() - Method in class etomica.normalmode.CoordinateDefinition
getSites(ISpace) - Static method in class etomica.models.water.P2WaterSzalewicz
getSitesNotParticipating(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
getSitesOnSpecies() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSize() - Method in class etomica.graphics.DisplayBox: Gets the size of the box graphic.
getSize() - Method in class etomica.lattice.crystal.Primitive: Returns a new array with values equal to the lengths of the primitive vectors.
getSize() - Method in interface etomica.lattice.FiniteLattice: Returns an array with elements giving the maximum number of index values in each dimension.
getSize() - Method in class etomica.lattice.RectangularLattice
getSizeA() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
getSizeA() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
getSizeA() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
getSizeA() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
getSizeAB() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
getSizeAB() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
getSizeAB() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
getSizeABC() - Method in class etomica.lattice.crystal.PrimitiveCubic: Returns the common length of all primitive vectors.
getSizeB() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
getSizeB() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
getSizeB() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
getSizeC() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
getSizeC() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
getSizeC() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
getSizeC() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
getSizeC() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
getSizeIncreaseRatio() - Static method in class etomica.atom.AtomArrayList
getSizeIncreaseRatio() - Static method in class etomica.atom.MoleculeArrayList
getSkewLog() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Returns the standard deviation of the log of the block averages, for all block sizes.
getSlab() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Get depth percentage
getSlab() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Get depth percentage
getSlab() - Method in class org.jmol.util.GData: gets g3d slab
getSlabColor() - Method in class org.jmol.util.MeshSurface
getSlabObject(int, Object, boolean, Object) - Static method in class org.jmol.util.MeshSurface
getSlabPercent() - Method in class g3dsys.control.G3DSys
getSlabTranslucency() - Method in class org.jmol.util.MeshSurface
getSlabType() - Method in class org.jmol.util.MeshSurface
getSlabWithinRange(float, float) - Static method in class org.jmol.util.MeshSurface
getSleepPeriod() - Method in class etomica.action.activity.ActivityIntegrate: Amount of time that thread is kept in sleep state after each doStep done on integrator.
getSlider(String) - Method in class etomica.graphics.DevicePlotPoints: Returns the slider for the given parameter.
getSlider() - Method in class etomica.graphics.DeviceSlider
getSlitDim() - Method in class etomica.space.BoundaryRectangularSlit: Returns index of non-periodic dimension.
getSnapshotTime() - Method in class etomica.graph.view.rasterizer.SVGConverter: Returns the document to to seek to before rasterizing.
getSoluteMoleFraction() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getSoluteMoleFraction() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: Returns the mole fraction of solutes within the solute chamber.
getSolutionChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getSolutionChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: Returns the number density of the solution chamber
getSolventChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getSolventChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater: Returns the number density of the solvent chamber
getSolventThermoFrac() - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: Returns the fraction of well energy that is gained or lost by an atom pair when they hop in or leave their well.
getSource() - Method in class etomica.integrator.IntegratorEvent
getSources() - Method in class etomica.graph.view.rasterizer.SVGConverter
getSpace() - Method in class etomica.config.ConfigurationLattice.MyLattice
getSpace() - Method in class etomica.data.types.DataTensor.DataInfoTensor
getSpace() - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory: Returns the Space
getSpace() - Method in class etomica.data.types.DataVector.DataInfoVector
getSpace() - Method in class etomica.data.types.DataVector.DataInfoVectorFactory: Returns the Space
getSpace() - Method in class etomica.lattice.BravaisLattice
getSpace() - Method in class etomica.lattice.crystal.Primitive
getSpace() - Method in interface etomica.lattice.SpaceLattice
getSpace() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
getSpace() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
getSpace() - Method in class etomica.simulation.Simulation
getSpace() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
getSpace() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getSpace() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getSpace() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getSpace() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
getSpacePosition() - Method in class etomica.lattice.LatticePlane: Gets the position of the plane as the distance from the origin in the direction of the normal.
getSpecialAtomName(int) - Static method in class org.jmol.viewer.JmolConstants
getSpecies() - Method in interface etomica.api.IAtomType
getSpecies() - Method in interface etomica.api.IBoxMoleculeCountEvent
getSpecies(int) - Method in interface etomica.api.ISimulation: Returns the Species in the Simulation for the specified index.
getSpecies() - Method in interface etomica.api.ISimulationSpeciesEvent
getSpecies() - Method in class etomica.atom.AtomTypeLeaf
getSpecies() - Method in class etomica.box.BoxMoleculeCountEvent
getSpecies() - Method in class etomica.chem.models.Model: Returns the species associated with this Model, if it has already been created.
getSpecies() - Method in class etomica.data.DataSourcePositionedBoltzmannFactor: Returns the ISpecies for which the chemical potential is to be measured.
getSpecies() - Method in class etomica.data.meter.MeterDensity
getSpecies() - Method in class etomica.data.meter.MeterLocalMoleFraction: Accessor method to get the current value of the species index
getSpecies() - Method in class etomica.data.meter.MeterMoleFraction
getSpecies() - Method in class etomica.data.meter.MeterNMolecules
getSpecies() - Method in class etomica.data.meter.MeterProfileByAtoms
getSpecies() - Method in class etomica.data.meter.MeterProfileByVolume
getSpecies() - Method in class etomica.data.meter.MeterWidomInsertion: Accessor for the species for which chemical potential is evaluated
getSpecies() - Method in class etomica.graphics.DeviceNSelector
getSpecies() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
getSpecies() - Method in class etomica.integrator.mcmove.MCMoveSemigrand: Accessor method for the set of species that can participate in an exchange move.
getSpecies() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Accessor for the species for which chemical potential is evaluated
getSpecies() - Method in class etomica.liquidLJ.MeterWidomInsertionP: Accessor for the species for which chemical potential is evaluated
getSpecies() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
getSpecies() - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
getSpecies() - Method in class etomica.modules.rosmosis.MeterFlux
getSpecies() - Method in class etomica.nbr.molecule.CriterionSpecies: Returns the Species accepted by this criterion.
getSpecies() - Method in class etomica.nbr.molecule.CriterionSpeciesPair: Returns the Species accepted by this NeighborCriterionMolecular
getSpecies() - Method in class etomica.normalmode.DeviceCellNum3DSlider
getSpecies() - Method in class etomica.normalmode.DeviceCellNumXYSlider
getSpecies() - Method in class etomica.parser.ParmedStructure
getSpecies(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
getSpecies(int) - Method in class etomica.simulation.Simulation
getSpecies() - Method in class etomica.simulation.SimulationSpeciesEvent
getSpecies() - Method in class etomica.species.Species
getSpecies(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getSpecies1() - Method in class etomica.config.ConfigurationZincblende
getSpecies2() - Method in class etomica.config.ConfigurationZincblende
getSpeciesAFixed() - Method in class etomica.config.GrainBoundaryConfiguration
getSpeciesAgentClass() - Method in interface etomica.atom.AtomTypeAgentManager.AgentSource: Returns the Class of the agent.
getSpeciesAgentClass() - Method in class etomica.atom.DiameterHashByType
getSpeciesAgentClass() - Method in interface etomica.atom.SpeciesAgentManager.AgentSource: Returns the Class of the agent.
getSpeciesAgentClass() - Method in class etomica.graphics.ColorSchemeByType
getSpeciesAgentClass() - Method in class etomica.integrator.IntegratorHard
getSpeciesAgentClass() - Method in class etomica.integrator.IntegratorRigidIterative
getSpeciesAgentClass() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
getSpeciesAgentClass() - Method in class etomica.integrator.IntegratorVelocityVerletShake
getSpeciesAgentClass() - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
getSpeciesAgentClass() - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
getSpeciesAgentClass() - Method in class etomica.nbr.PotentialMasterNbr
getSpeciesAgentClass() - Method in class etomica.potential.PotentialMasterMonatomic
getSpeciesAgentClass() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
getSpeciesAllocation(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane: Sets the initial allocation of the species on the left side of the plane.
getSpeciesAMobile() - Method in class etomica.config.GrainBoundaryConfiguration
getSpeciesBFixed() - Method in class etomica.config.GrainBoundaryConfiguration
getSpeciesBMobile() - Method in class etomica.config.GrainBoundaryConfiguration
getSpeciesco2Potentialslist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesCount() - Method in interface etomica.api.ISimulation: Returns the number of Species in the Simulation.
getSpeciesCount() - Method in class etomica.simulation.Simulation
getSpeciesCount1() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getSpeciesCount2() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getSpeciesCount3() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getSpeciesDataModel(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getSpeciesDataModel() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getSpeciesDM() - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
getSpeciesethanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesh2oPotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesID() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
getSpeciesID() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
getSpeciesID() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
getSpeciesIdentifier(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
getSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
getSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
getSpeciesInteractionIndex() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getSpeciesJList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getSpeciesJList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getSpeciesJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getSpeciesJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getSpeciesList() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesListDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
getSpeciesListDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getSpeciesljPotentialslist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesMembrane() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getSpeciesMembrane() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
getSpeciesmethanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesMoleculeCount(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getSpeciesMoleculeCount() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
getSpeciesnalkanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciespropanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesRemovalMsgBox() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getSpeciesSelectedIndex() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesSelectedIndex(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
getSpeciesSelectionDM() - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
getSpeciesSolute() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getSpeciesSolute1() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
getSpeciesSolute2() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
getSpeciesSolvent() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
getSpeciesSolvent() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
getSpecular() - Static method in class org.jmol.util.GData
getSpecularExponent() - Static method in class org.jmol.util.GData
getSpecularPercent() - Static method in class org.jmol.util.GData
getSpecularPower() - Static method in class org.jmol.util.GData
getSphereData(int) - Static method in class org.jmol.util.MeshSurface: Calculates the data (faces, vertices, normals) for a sphere.
getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
getSpinner() - Method in class etomica.graphics.DeviceSpinner
getSpinnerPanel() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
getSplines() - Method in class etomica.potential.P2QChemInterpolated
getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
getSplitDisconnectedVirialGraphs(Graph) - Method in class etomica.virial.cluster.VirialDiagrams
getSplitDisconnectedVirialGraphs(Graph) - Method in class etomica.virial.cluster.VirialDiagramsMix2
getSplitDisconnectedVirialGraphs(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT
getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialAlkaneFull
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCH4AlkaneEHMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCO2AlkaneEHMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCO2AlkaneUAMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCO2N2Mix
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialCO2PI
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialH2PI
getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialHePI
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialN2AlkaneEHMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialN2AlkaneUAMix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialN2CH4Mix
getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix
getSpringConstant() - Method in class etomica.modules.materialfracture.P1Tension
getSpringConstant() - Method in class etomica.potential.P1Harmonic
getSpringConstant() - Method in class etomica.potential.P1HarmonicSite
getSpringConstant() - Method in class etomica.potential.P2Anharmonic: Accessor method for harmonic energy parameter
getSpringConstant() - Method in class etomica.potential.P2Harmonic: Accessor method for harmonic energy parameter
getSpringConstantDimension() - Method in class etomica.modules.materialfracture.P1Tension: Not implemented correctly.
getSpringConstantDimension() - Method in class etomica.potential.P1Harmonic
getSpringConstantDimension() - Method in class etomica.potential.P1HarmonicSite
getSpringConstantDimension() - Method in class etomica.potential.P2Anharmonic: Not implemented correctly.
getSpringConstantDimension() - Method in class etomica.potential.P2Harmonic: Not implemented correctly.
getSqErr(double[], double[]) - Method in class etomica.modules.interfacial.FitTanh
getSqErr(double[], double[]) - Method in class etomica.surfacetension.FitTanh
getStandardPdbHydrogenCount(int) - Static method in class org.jmol.viewer.JmolConstants
getStart() - Method in class g3dsys.images.Line
getStartAtom() - Method in class etomica.virial.MCMoveClusterAtomMulti
getState() - Method in class etomica.graphics.DeviceCheckBox: Returns the currents true/false state of the button.
getState() - Method in class etomica.graphics.DeviceToggleButton: Returns the current true/false state of the button.
getState() - Method in class etomica.graphics.DeviceToggleRadioButtons: Returns the currents true/false state of the button.
getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.ApiPlatform
getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
getStdev() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Returns the standard deviation of the block averages, for all block sizes.
getStdevantibiasedLog() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB: Returns the standard deviation of the log of the block averages, for all block sizes.
getStdevLog() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Returns the standard deviation of the log of the block averages, for all block sizes.
getStepCount() - Method in interface etomica.api.IIntegrator: Returns the number of steps performed by the integrator since it was initialized.
getStepCount() - Method in class etomica.integrator.Integrator: Returns the number of steps performed by the integrator since it was initialized.
getStepFreq0() - Method in class etomica.virial.overlap.IntegratorOverlap
getStepSize() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
getStepSize() - Method in class etomica.integrator.mcmove.MCMoveStep
getStepSize() - Method in interface etomica.integrator.mcmove.MCMoveStepDependent: returns the current step size.
getStepSizeDimension() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
getStepSizeDimension() - Method in class etomica.integrator.mcmove.MCMoveStep
getStepSizeMax() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
getStepSizeMax() - Method in class etomica.integrator.mcmove.MCMoveStep
getStepSizeMax() - Method in interface etomica.integrator.mcmove.MCMoveStepDependent: Returns the maximum allowable steps size.
getStepSizeMaxDimension() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
getStepSizeMaxDimension() - Method in class etomica.integrator.mcmove.MCMoveStep
getStepSizeMin() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
getStepSizeMin() - Method in class etomica.integrator.mcmove.MCMoveStep
getStepSizeMin() - Method in interface etomica.integrator.mcmove.MCMoveStepDependent: Returns the minimum allowable steps size.
getStepSizeMinDimension() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
getStepSizeMinDimension() - Method in class etomica.integrator.mcmove.MCMoveStep
getStereoMode(String) - Static method in enum org.jmol.constant.EnumStereoMode
getStiffness() - Method in class etomica.virial.MCMoveChangeBondLength
getStiffness() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
getStockComponent(char, char) - Static method in class etomica.graph.model.impl.MetadataImpl
getStore() - Method in interface etomica.graph.model.Graph
getStore() - Method in class etomica.graph.model.impl.GraphImpl
getStrands() - Method in class etomica.graph.property.FFTDecomposition
getStrands() - Method in class etomica.graph.property.IsFFT
getSType() - Method in class etomica.virial.Species7SiteRigidSF6
getSubCluster() - Method in class etomica.virial.ClusterCoupledFlipped
getSubCluster() - Method in class etomica.virial.ClusterCoupledFlippedPartial
getSubCluster() - Method in class etomica.virial.ClusterWeightAbs
getSubDataInfo() - Method in class etomica.data.DataSourceGroup
getSubDataInfo(int) - Method in class etomica.data.types.DataGroup.DataInfoGroup: Returns the DataInfo corresponding to the group's given wrapped Data object.
getSubDataInfo() - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
getSubIntegrator() - Method in class etomica.thermointegration.IntegratorThermodynamic: Returns the subIntegrator, responsible for actually walking through configurational space.
getSulfurType() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
getSum() - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
getSum() - Method in class etomica.normalmode.PotentialCalculationEFSSP: Returns the current value of the energy sum.
getSum() - Method in class etomica.normalmode.PotentialCalculationLJSP: Returns the current value of the energy sum.
getSum() - Method in class etomica.potential.PotentialCalculationEnergySum: Returns the current value of the energy sum.
getSum() - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal: Returns the current value of the energy sum.
getSum() - Method in class etomica.potential.PotentialCalculationHyperVirialSum: Returns the current value of the energy sum.
getSum() - Method in class etomica.potential.PotentialCalculationMolecularVirialSum: Returns the current value of the energy sum.
getSum() - Method in class etomica.potential.PotentialCalculationPhiSum: Returns the current value of the energy sum.
getSum() - Method in class etomica.potential.PotentialCalculationVirialSum: Returns the current value of the energy sum.
getSum1() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
getSum2() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
getSums() - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff: Returns the current value of the energy sum.
getSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoffLS: Returns the current value of the energy sum.
getSurfaceArea() - Method in class etomica.math.geometry.Cube: Returns 6*edgeLength^2
getSurfaceArea() - Method in class etomica.math.geometry.Cuboid
getSurfaceArea() - Method in class etomica.math.geometry.Parallelepiped
getSurfaceArea() - Method in class etomica.math.geometry.Polyhedron: Returns the sum the area of the faces of the polyhedron
getSurfaceColor() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
getSurfaceDimension() - Method in class etomica.data.DataProcessorInterfacialTension: Returns the dimension of the surfaces.
getSurfaceYOffset() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
getSurfaceYOffset() - Method in class etomica.modules.sam.ConfigurationSAM
getSweepRadius() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
getSwitchFac() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
getSwitchFac() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
getSymbol() - Method in interface etomica.api.IElement
getSymbol() - Method in class etomica.chem.elements.Element
getSymbols() - Method in class etomica.graphics.DeviceTernarySelector: Accessor method for the symbols.
getSystemSigmaHSRef() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getT1() - Method in class etomica.normalmode.HTTPSoftSphereApplet
getT2() - Method in class etomica.normalmode.HTTPSoftSphereApplet
getTableModel() - Method in class etomica.graphics.DevicePlotPoints
getTableUpdateInterval() - Method in class etomica.data.DataTableAverages
getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorAverage
getTag(AccumulatorAverageBlockless.StatType) - Method in class etomica.data.AccumulatorAverageBlockless
getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorRatioAverage
getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorRatioAverageCovariance
getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
getTag() - Method in class etomica.data.DataDistributer: Returns the DataTag associated with this DataSplitter
getTag() - Method in class etomica.data.DataDump
getTag() - Method in class etomica.data.DataFork
getTag() - Method in class etomica.data.DataGroupSplitter: Returns the DataTag associated with this DataGroupSplitter
getTag() - Method in interface etomica.data.DataPipe
getTag() - Method in class etomica.data.DataProcessor
getTag() - Method in interface etomica.data.DataSourceAtomic
getTag() - Method in class etomica.data.DataSourceFunction
getTag() - Method in class etomica.data.DataSourceGroup
getTag() - Method in interface etomica.data.DataSourceMolecular
getTag() - Method in class etomica.data.DataSourcePoints
getTag() - Method in interface etomica.data.DataSourcePositioned
getTag() - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
getTag() - Method in class etomica.data.DataSourceRmsVelocity
getTag() - Method in class etomica.data.DataSourceScalar
getTag() - Method in class etomica.data.DataSourceTensorVirialHard
getTag() - Method in class etomica.data.DataSourceUniform
getTag() - Method in class etomica.data.DataSplitter: Returns the DataTag associated with this DataSplitter
getTag() - Method in class etomica.data.HistogramDataSource
getTag() - Method in interface etomica.data.IEtomicaDataSource
getTag() - Method in class etomica.data.meter.MeterDihedralAngle
getTag() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
getTag() - Method in class etomica.data.meter.MeterHyperVirial
getTag() - Method in class etomica.data.meter.MeterMomentumCOM
getTag() - Method in class etomica.data.meter.MeterPositionCOM
getTag() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
getTag() - Method in class etomica.data.meter.MeterPressureByVolumeChange
getTag() - Method in class etomica.data.meter.MeterPressureHardTensor
getTag() - Method in class etomica.data.meter.MeterPressureTensor
getTag() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
getTag() - Method in class etomica.data.meter.MeterProfile
getTag() - Method in class etomica.data.meter.MeterProfileByAtoms
getTag() - Method in class etomica.data.meter.MeterProfileByVolume
getTag() - Method in class etomica.data.meter.MeterRDF
getTag() - Method in class etomica.data.meter.MeterRDFPC
getTag() - Method in class etomica.data.meter.MeterTensorVelocity
getTag() - Method in class etomica.freeenergy.npath.DataSourceEnergies
getTag() - Method in class etomica.gaussianwork.MeterBoltzmannA
getTag() - Method in class etomica.gaussianwork.MeterBoltzmannB
getTag() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getTag() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getTag() - Method in class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
getTag() - Method in class etomica.integrator.IntegratorPT.BoxTracker
getTag() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
getTag() - Method in class etomica.liquidLJ.MeterPU
getTag() - Method in class etomica.liquidLJ.MeterPUCut
getTag() - Method in class etomica.liquidLJ.MeterPUCutLS
getTag() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
getTag() - Method in class etomica.mappedvirial.MeterMeanForce
getTag() - Method in class etomica.metastable.MeterDensityDistribution
getTag() - Method in class etomica.models.nitrogen.MeterBoltzmann
getTag() - Method in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
getTag() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
getTag() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
getTag() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
getTag() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
getTag() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getTag() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getTag() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
getTag() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
getTag() - Method in class etomica.models.oneDHardRods.MeterOverlap
getTag() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
getTag() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
getTag() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
getTag() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
getTag() - Method in class etomica.modules.chainequilibrium.MeterChainLength
getTag() - Method in class etomica.modules.droplet.MeterDeformation
getTag() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
getTag() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
getTag() - Method in class etomica.modules.interfacial.MeterOrientation
getTag() - Method in class etomica.modules.mu.DataSourceWallPressureMu
getTag() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
getTag() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
getTag() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
getTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
getTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
getTag() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
getTag() - Method in class etomica.modules.rosmosis.MeterFlux
getTag() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
getTag() - Method in class etomica.modules.sam.MeterTilt
getTag() - Method in class etomica.normalmode.DataSourceFE
getTag() - Method in class etomica.normalmode.DataSourceFEHistogram
getTag() - Method in class etomica.normalmode.DataSourceImposedFEFit
getTag() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
getTag() - Method in class etomica.normalmode.DataSourcePMu
getTag() - Method in class etomica.normalmode.DataSourcePN
getTag() - Method in class etomica.normalmode.MeterAtomicDisplacement
getTag() - Method in class etomica.normalmode.MeterBoltzmann
getTag() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
getTag() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getTag() - Method in class etomica.normalmode.MeterBoltzmannTarget
getTag() - Method in class etomica.normalmode.MeterDADB
getTag() - Method in class etomica.normalmode.MeterDDP
getTag() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
getTag() - Method in class etomica.normalmode.MeterDirectSamplingTarget
getTag() - Method in class etomica.normalmode.MeterDP
getTag() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
getTag() - Method in class etomica.normalmode.MeterNormalMode
getTag() - Method in class etomica.normalmode.MeterOverlapSwitch
getTag() - Method in class etomica.normalmode.MeterPlaneSlip
getTag() - Method in class etomica.normalmode.MeterSamplingHarmonic
getTag() - Method in class etomica.normalmode.MeterSamplingTarget
getTag() - Method in class etomica.normalmode.MeterSolidDA
getTag() - Method in class etomica.normalmode.MeterSolidDACut
getTag() - Method in class etomica.normalmode.MeterSolidMirror
getTag() - Method in class etomica.normalmode.MeterSolidProps
getTag() - Method in class etomica.normalmode.MeterSolidPropsLJ
getTag() - Method in class etomica.normalmode.MeterTargetTP
getTag() - Method in class etomica.normalmode.MeterTilt
getTag() - Method in class etomica.normalmode.MeterTiltHistogram
getTag() - Method in class etomica.normalmode.MeterTiltRotation
getTag() - Method in class etomica.normalmode.MeterTiltRotationHistogram
getTag(int) - Method in class etomica.normalmode.MeterTiltRotationHistogram
getTag() - Method in class etomica.normalmode.MeterTiltRotationStdev
getTag() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
getTag() - Method in class etomica.normalmode.MeterWorkBennetTarget
getTag() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
getTag() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
getTag() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getTag() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
getTag() - Method in class etomica.normalmode.MeterWorkTargetBennet
getTag() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
getTag() - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
getTag() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
getTag() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
getTag() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
getTag() - Method in class etomica.overlap.MeterOverlap
getTag() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
getTag() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
getTag() - Method in class etomica.virial.MeterSamplingWeight
getTag() - Method in class etomica.virial.MeterVirial
getTag() - Method in class etomica.virial.MeterVirialBD
getTag() - Method in class etomica.virial.MeterVirialBDBin
getTag() - Method in class etomica.virial.MeterVirialExternalField
getTag() - Method in class etomica.virial.MeterVirialExternalFieldConfined
getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
getTag() - Method in class etomica.virial.MeterVirialExternalFieldRho
getTag() - Method in class etomica.virial.MeterVirialExternalFieldSW
getTag() - Method in class etomica.virial.MeterVirialIC
getTag() - Method in class etomica.virial.MeterVirialSWWE
getTags() - Method in class etomica.data.DataInfo: Returns the array of tags held by this DataInfo instance.
getTags() - Method in class etomica.data.DataInfoFactory
getTags() - Method in interface etomica.data.IEtomicaDataInfo: Returns the array of tags held by this DataInfo instance.
getTags() - Method in interface etomica.data.IEtomicaDataInfoFactory: Returns the factory's tags as an array.
getTargetAtom() - Method in class etomica.atom.iterator.IteratorDirective
getTargetCluster() - Method in class etomica.virial.MeterVirialBDBin
getTargetCluster() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
getTargetCluster() - Method in class etomica.virial.MeterVirialBinMultiThreaded
getTargetCluster() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
getTargetDataInterval() - Method in class etomica.normalmode.SimOverlapModule
getTargetDensity() - Method in class etomica.action.BoxInflate: Returns the target density of the action.
getTargetH() - Method in class etomica.integrator.IntegratorGear4NPH
getTargetHDimension() - Method in class etomica.integrator.IntegratorGear4NPH
getTargetMolecule() - Method in class etomica.atom.iterator.IteratorDirective
getTargetP() - Method in class etomica.integrator.IntegratorGear4NPH
getTargetPDimension() - Method in class etomica.integrator.IntegratorGear4NPH
getTargetSource() - Method in class etomica.overlap.DataOverlap: Returns object capable of retrieving data from the target system.
getTargetT() - Method in class etomica.integrator.IntegratorGear4NPH
getTargetTDimension() - Method in class etomica.integrator.IntegratorGear4NPH
getTemperature() - Method in class etomica.action.AtomActionRandomizeVelocity
getTemperature() - Method in class etomica.action.BoxQuench: Returns the quench temperature.
getTemperature() - Method in class etomica.action.BoxRandomizeMomenta
getTemperature() - Method in class etomica.action.BoxScaleMomenta
getTemperature() - Method in class etomica.gaussianwork.MeterBoltzmannA
getTemperature() - Method in class etomica.gaussianwork.MeterBoltzmannB
getTemperature() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
getTemperature() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
getTemperature() - Method in class etomica.graphics.DeviceThermoSlider
getTemperature() - Method in class etomica.integrator.IntegratorBox
getTemperature() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
getTemperature() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
getTemperature() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
getTemperature() - Method in class etomica.normalmode.BoltzmannProcessor
getTemperature() - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
getTemperature() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
getTemperature() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
getTemperature() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
getTemperature() - Method in class etomica.normalmode.MeterBoltzmannHTTP
getTemperature() - Method in class etomica.normalmode.MeterDDP
getTemperature() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
getTemperature() - Method in class etomica.normalmode.MeterDP
getTemperature() - Method in class etomica.normalmode.MeterTargetTP
getTemperature() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
getTemperature() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
getTemperature() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
getTemperature() - Method in class etomica.potential.P2LJDipole
getTemperature() - Method in class etomica.potential.P2LJQ
getTemperature() - Method in class etomica.potential.P2LJQQ
getTemperature() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
getTemperature() - Method in class etomica.virial.ClusterSum
getTemperature() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
getTemperature() - Method in class etomica.virial.ClusterSumPolarizable
getTemperature() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
getTemperature() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
getTemperature() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
getTemperature() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
getTemperature() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
getTemperatureDimension() - Method in class etomica.integrator.IntegratorBox
getTemperatureDimension() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
getTemperatureField() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
getTemperatureSource() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT: Returns the temperature data source.
getTetherLength() - Method in class etomica.potential.P2Tether: Accessor method for the tether distance
getTetherLengthDimension() - Method in class etomica.potential.P2Tether
getTextBackground() - Method in class etomica.graphics.DeviceBox
getTextField() - Method in class etomica.graphics.DeviceSlider
getTextPixels(String, JmolFont, Object, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
getTextPixels(String, JmolFont, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
getThermostat() - Method in class etomica.integrator.IntegratorMD
getThermostatInterval() - Method in class etomica.integrator.IntegratorMD
getTheta() - Method in class etomica.association.BiasVolumeSphereOriented
getTheta() - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
getTheta() - Method in class etomica.models.water.P2HardAssociationGCPMReference
getTheta() - Method in class etomica.models.water.PNWaterGCPMThreeSite
getTheta() - Method in class etomica.potential.P2HardAssociationCone: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeReference: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for angle describing width of cone.
getTheta() - Method in class etomica.potential.P2QChemInterpolated
getTheta() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getTheta() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getTheta() - Method in class org.jmol.util.Quaternion
getThetaDimension() - Method in class etomica.potential.P2HardAssociationCone
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeFourSites
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeOneSite
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeReference
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeSW
getThetaDirected(Point4f) - Method in class org.jmol.util.Quaternion
getThetaDirectedV(Vector3f) - Method in class org.jmol.util.Quaternion
getThetaFrac() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
getThetaRadians() - Method in class org.jmol.util.Quaternion
getTHigh() - Method in class etomica.graphics.ColorSchemeTemperature
getTilt() - Method in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
getTilt() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
getTimeDataSource() - Method in class etomica.data.AccumulatorHistory: Returns the DataSource used for the "time" component of the history.
getTimer() - Method in class etomica.graphics.DisplayTimer: Returns the data source used to count the time, to permit access to its methods for reset, etc.
getTimeStep() - Method in class etomica.integrator.IntegratorMD
getTimeStepDimension() - Method in class etomica.integrator.IntegratorMD
getTitle() - Method in class etomica.graphics.DeviceToggleRadioButtons
getTLow() - Method in class etomica.graphics.ColorSchemeTemperature
getTLowDimension() - Method in class etomica.graphics.ColorSchemeTemperature
getTM() - Method in class g3dsys.control.G3DSys
getTokenFromName(String) - Static method in class org.jmol.script.Token
getTokens(String) - Static method in class org.jmol.util.Parser
getTokensAt(String, int) - Static method in class org.jmol.util.Parser
getTokensLike(String) - Static method in class org.jmol.script.Token
getTokFromName(String) - Static method in class org.jmol.script.Token
getTolerance() - Method in class etomica.modules.interfacial.FitTanh
getTolerance() - Method in class etomica.surfacetension.FitTanh
getToNode(byte) - Method in interface etomica.graph.model.Graph
getToNode(byte) - Method in class etomica.graph.model.impl.GraphImpl
getToPixels() - Method in class etomica.graphics.DisplayBox
getToPixels() - Method in class etomica.graphics.DisplayPolytope
getTorsionpotentiala0() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala0() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getTorsionpotentiala1() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala1() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getTorsionpotentiala2() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala2() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getTorsionpotentiala3() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
getTorsionpotentiala3() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
getTotalCount() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
getTotalCount() - Method in class etomica.virial.MeterVirialBinMultiThreaded
getTotalCount() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
getTracker() - Method in class etomica.integrator.mcmove.MCMove
getTranscoder() - Method in class etomica.graph.view.rasterizer.DestinationType: Returns a transcoder object of the result image type.
getTransformationTensor() - Method in class etomica.models.nitrogen.AtomActionTransformed
getTransformationTensor() - Method in class etomica.paracetamol.AtomActionTransformed
getTransformedVertexVectors() - Method in class org.jmol.g3d.Graphics3D
getTransformedVertexVectors() - Method in class org.jmol.util.GData
getTransformMatrix4(List<Point3f>, List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
getTranslationVector() - Method in class etomica.action.AtomActionTranslateBy: Returns the translation vector, the distance that the atom will be moved by this action.
getTranslationVector() - Method in class etomica.action.MoleculeActionTranslateTo: Returns the vector that was used to accomplish the most recent translation action.
getTrimThreshold() - Method in class etomica.atom.AtomArrayList
getTrimThreshold() - Method in class etomica.atom.MoleculeArrayList
getTrueLabel() - Method in class etomica.action.ActionToggle
getTrueLabel() - Method in class etomica.graphics.DeviceToggleButton
getTrueLabel() - Method in class etomica.graphics.DeviceToggleRadioButtons
getTruncatedPotential() - Method in class etomica.potential.Potential0Lrc: Returns the potential whose truncation this lrcPotential exists to correct.
getTruncation() - Method in class etomica.potential.PotentialGroupSoft
getTruncationRadius() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched: Accessor method for the radial cutoff distance.
getTruncationRadius() - Method in class etomica.potential.P2MoleculeTruncated: Accessor method for the radial cutoff distance.
getTruncationRadius() - Method in class etomica.potential.P2SoftSphericalTruncated: Accessor method for the radial cutoff distance.
getTruncationRadius() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched: Accessor method for the radial cutoff distance.
getTruncationRadius() - Method in class etomica.potential.P2SoftTruncated: Accessor method for the radial cutoff distance.
getTruncationRadius() - Method in class etomica.space.BoundaryDeformablePeriodic
getTruncationRadiusDimension() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched: Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() - Method in class etomica.potential.P2MoleculeTruncated: Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched: Returns the dimension (length) of the radial cutoff distance.
getTruncationRadiusDimension() - Method in class etomica.potential.P2SoftTruncated: Returns the dimension (length) of the radial cutoff distance.
getTSelement() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
getTunable() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
getType() - Method in class etomica.action.activity.ControllerEvent
getType() - Method in interface etomica.api.IAtom
getType() - Method in interface etomica.api.IMolecule: Returns the ISpecies of this IMolecule.
getType() - Method in class etomica.atom.Atom
getType() - Method in class etomica.atom.Molecule
getType() - Method in interface etomica.graph.model.Edge
getType() - Method in class etomica.graph.model.impl.EdgeImpl
getType() - Method in class etomica.graph.model.impl.MetadataImpl
getType() - Method in class etomica.graph.model.impl.NodeImpl
getType() - Method in interface etomica.graph.model.Metadata
getType() - Method in interface etomica.graph.model.Node
getType() - Method in class etomica.nbr.CriterionType: Returns the AtomType accepted by this criterion.
getTypeInteraction() - Method in class etomica.action.WriteConfigurationP2DLPOLY
getTypeMax() - Method in class etomica.data.DataSourceUniform: Accessor method for the type of the right limit.
getTypeMin() - Method in class etomica.data.DataSourceUniform: Accessor method for the type of the left limit.
getTypes() - Method in class etomica.nbr.CriterionTypePair: Returns the AtomTypes accepted by this NeighborCriterion
getTypes() - Method in class etomica.nbr.CriterionTypesCombination: Returns the AtomTypes accepted by this NeighborCriterion
getTypes() - Method in class etomica.nbr.CriterionTypesMulti: Returns the AtomTypes accepted by this NeighborCriterion
getTypes() - Method in class etomica.potential.PotentialArrayByType
getU123ADD(P2QChemInterpolated, double, double, double) - Method in class etomica.potential.P3AdditiveQChem
getU123SCF(double, double, int) - Method in class etomica.potential.P3QChem
getUa2(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2: Returns average value of expression used to determine optimal Bennet parameter (value[1]/(value[1]+expX[iParam]).
getUDisp(double) - Method in class etomica.potential.P2QChemInterpolated
getUlat0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
getUlat0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
getULatFunction() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
getULatFunction() - Method in class etomica.normalmode.MCMoveVolumeSolid
getULatFunction() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
getULatFunction() - Method in class etomica.normalmode.MeterDDP
getULatFunction() - Method in class etomica.normalmode.MeterDP
getULatTruncFunction() - Method in class etomica.normalmode.MCMoveVolumeSolid
getUnit() - Method in class etomica.graphics.Device
getUnit() - Method in class etomica.graphics.DimensionedDoubleEditor
getUnit() - Method in class etomica.graphics.DisplayScrollingGraph: Returns the physical units of the displayed value.
getUnit(int) - Method in class etomica.graphics.DisplayTable: Returns the unit assign to the i-th column (as defined before any transpose).
getUnit() - Method in class etomica.graphics.DisplayTextBox: Returns the physical units of the displayed value.
getUnit() - Method in class etomica.graphics.DisplayTextBoxesCAE
getUnit(UnitSystem) - Method in class etomica.units.Angle
getUnit(UnitSystem) - Method in class etomica.units.Area
getUnit(UnitSystem) - Method in class etomica.units.Charge
getUnit(UnitSystem) - Method in class etomica.units.CompoundDimension
getUnit(UnitSystem) - Method in class etomica.units.Current
getUnit(UnitSystem) - Method in class etomica.units.Dimension: Returns the unit of this dimension as derived in the given system of units.
getUnit() - Method in interface etomica.units.Dimensioned
getUnit(UnitSystem) - Method in class etomica.units.DimensionRatio
getUnit(UnitSystem) - Method in class etomica.units.Dipole
getUnit(UnitSystem) - Method in class etomica.units.ElectricPotential
getUnit(UnitSystem) - Method in class etomica.units.Energy
getUnit(UnitSystem) - Method in class etomica.units.Force
getUnit(UnitSystem) - Method in class etomica.units.Fraction
getUnit(UnitSystem) - Method in class etomica.units.Length
getUnit(UnitSystem) - Method in class etomica.units.LuminousIntensity
getUnit(UnitSystem) - Method in class etomica.units.Mass
getUnit(UnitSystem) - Method in class etomica.units.Null: Returns UNIT, regardless of the given unit system.
getUnit(UnitSystem) - Method in class etomica.units.Pressure
getUnit(UnitSystem) - Method in class etomica.units.Pressure2D
getUnit(UnitSystem) - Method in class etomica.units.Quantity
getUnit(UnitSystem) - Method in class etomica.units.Temperature
getUnit(UnitSystem) - Method in class etomica.units.Time
getUnit(UnitSystem) - Method in class etomica.units.Undefined: Returns UNIT, regardless of the given unit system.
getUnit(UnitSystem) - Method in class etomica.units.Viscosity
getUnit(UnitSystem) - Method in class etomica.units.Volume
getUnitVectors(double[][], Vector3f[], float[]) - Static method in class org.jmol.util.Eigen
getUnscreenedCount() - Method in class etomica.virial.MeterVirialBDBin
getUpdatedDimensions() - Method in class etomica.zeolite.ConfigurationFileXYZ
getUpdateInterval() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Returns the interval for which neighbor update checks are performed.
getUpdateInterval() - Method in class etomica.nbr.list.NeighborListManager: Returns the interval for which neighbor update checks are performed.
getUpList() - Method in class etomica.nbr.list.AtomNeighborLists: Returns an array of uplist-neighbor-atom lists.
getUpList() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists: Returns an array of uplist-neighbor-molecule lists.
getUpList(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
getUpList(IAtom) - Method in class etomica.nbr.list.NeighborListManager
getUpperLimit() - Method in class etomica.models.hexane.SpeciesHexane
getUpsilon(int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
getUpsilon(int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
getuReactCO() - Method in class etomica.modules.catalysis.ReactionManagerCO
getuReactCORev() - Method in class etomica.modules.catalysis.ReactionManagerCO
getURI() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
getURI() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
getURI() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource: Returns a URI string corresponding to this source
getURI() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
getUSCF(double) - Method in class etomica.potential.P2QChemInterpolated
getUserStylesheet() - Method in class etomica.graph.view.rasterizer.SVGConverter
getUseSurfaceOnly() - Method in class etomica.modules.droplet.P2Cohesion
getUSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff: Returns the current value of the energy sum.
getV() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition: Return the eigenvector matrix
getV1() - Method in class etomica.models.hexane.ConformationHexane
getV2() - Method in class etomica.models.hexane.ConformationHexane
getVacancyFraction(double) - Method in class etomica.statmech.HardSphereSolid: Returns the fraction of lattice sites with a vacancy for the given lattice density.
getVacancyFreeEnergy(double) - Method in class etomica.statmech.HardSphereSolid: Returns the Helmholtz free energy difference due to the presence of vacancies at the given lattice density.
getVacancyPressure(double) - Method in class etomica.statmech.HardSphereSolid: Returns the difference between the pressure with vacancies from the pressure without vacancies for the given lattice density.
getValidate() - Method in class etomica.graph.view.rasterizer.SVGConverter
getValue(int, int) - Method in class etomica.data.DataSinkTable
getValue(int) - Method in interface etomica.data.IData: Returns the i-th data value.
getValue(int) - Method in class etomica.data.types.DataDouble: Returns this instance's value if argument is 0, otherwise throw exception
getValue(int) - Method in class etomica.data.types.DataDoubleArray: Returns the i-th value of the wrapped array.
getValue(int[]) - Method in class etomica.data.types.DataDoubleArray: Returns the element of the array indicated by the given set of indices.
getValue(int) - Method in class etomica.data.types.DataDoubleBDArray: Returns the i-th value of the wrapped array.
getValue(int[]) - Method in class etomica.data.types.DataDoubleBDArray: Returns the element of the array indicated by the given set of indices.
getValue(int) - Method in class etomica.data.types.DataGroup
getValue(int) - Method in class etomica.data.types.DataTable: Returns the i-th data value, where the values are numbered by counting down the first column, then the next, and so on.
getValue(int) - Method in class etomica.data.types.DataTensor: Returns the i-th tensor value, indexing across the first row, then the second, etc.
getValue(int) - Method in class etomica.data.types.DataVector: Returns the i-th vector value.
getValue() - Method in class etomica.graph.engine.impl.CommandPropertyValueImpl
getValue() - Method in class etomica.graph.engine.impl.CommandValueImpl
getValue() - Method in class etomica.graph.engine.impl.CommandVariableValueImpl
getValue() - Method in class etomica.graph.engine.impl.ValueImpl
getValue() - Method in interface etomica.graph.engine.Parser.CommandPropertyValue
getValue() - Method in interface etomica.graph.engine.Parser.CommandValue
getValue() - Method in interface etomica.graph.engine.Parser.CommandVariableValue
getValue() - Method in interface etomica.graph.engine.Parser.Value
getValue() - Method in interface etomica.graph.model.Coefficient
getValue() - Method in class etomica.graph.model.impl.CoefficientImpl
getValue() - Method in class etomica.graphics.DeviceBoxValueChangedEvent
getValue() - Method in class etomica.graphics.DeviceSlider
getValue() - Method in class etomica.graphics.DeviceSpinner
getValue() - Method in class etomica.graphics.DimensionedDoubleEditor: Returns the value in simulation units.
getValue() - Method in class etomica.liquidLJ.LjMd3D.ValueCache
getValue() - Method in class etomica.liquidLJ.ValueCache
getValue() - Method in interface etomica.modifier.Modifier: Gets the current value of the property.
getValue() - Method in class etomica.modifier.ModifierFunctionWrapper: Applies inverse of function to property before returning it.
getValue() - Method in class etomica.modifier.ModifierGeneral
getValue() - Method in class etomica.modifier.ModifierNMolecule
getValue() - Method in class etomica.modifier.ModifyAction
getValue() - Method in class etomica.modules.adsorption.ModifierPMu
getValue() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
getValue() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
getValue() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
getValue() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
getValue() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
getValue() - Method in class etomica.modules.entropylottery.ModifierDimensions
getValue() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
getValue() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
getValue() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
getValue() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
getValue() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
getValue() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
getValue() - Method in class etomica.normalmode.ModifierCells3D
getValue() - Method in class etomica.normalmode.ModifierXCells2D
getValue() - Method in class etomica.normalmode.ModifierYCells2D
getValue(String) - Method in class etomica.util.Grabber.ActionCornerSetter
getValue() - Method in class etomica.virial.simulations.ModifierTPI
getValueAt(int, int) - Method in class etomica.graphics.DeviceTableModelGeneric: Get the value in the given table cell.
getValueAt(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
getValueAt(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
getValueAt(int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
getValues() - Method in class etomica.graph.view.rasterizer.DestinationType: Defines valid image types.
getValueString(Field) - Method in class etomica.util.ParameterBase: Actually writes field name and value to a file using fileWriter.
getValueString(Object, Field) - Method in interface etomica.util.ParameterParser: Returns the value of obj's field as a string if this parser is appropirate for the given field, or throws an exception if it's not.
getVanderwaalsMar(int, EnumVdw) - Static method in class org.jmol.util.Elements
getVaporColor() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
getVar(MathContext) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
getVar() - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
getVar(int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
getVarDouble() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
getVariable() - Method in class etomica.graph.engine.impl.AssignmentImpl
getVariable() - Method in class etomica.graph.engine.impl.CommandVariableImpl
getVariable() - Method in class etomica.graph.engine.impl.CommandVariableValueImpl
getVariable() - Method in interface etomica.graph.engine.Parser.Assignment
getVariable() - Method in interface etomica.graph.engine.Parser.CommandVariable
getVariable() - Method in interface etomica.graph.engine.Parser.CommandVariableValue
getVariable(Object) - Static method in class org.jmol.script.ScriptVariable
getVariableAD(double[]) - Static method in class org.jmol.script.ScriptVariable
getVariableAF(float[]) - Static method in class org.jmol.script.ScriptVariable
getVariableAFF(float[][]) - Static method in class org.jmol.script.ScriptVariable
getVariableAI(int[]) - Static method in class org.jmol.script.ScriptVariable
getVariableAII(int[][]) - Static method in class org.jmol.script.ScriptVariable
getVariableAP(Point3f[]) - Static method in class org.jmol.script.ScriptVariable
getVariableAS(String[]) - Static method in class org.jmol.script.ScriptVariable
getVariableAV(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable
getVariableList(List<?>) - Static method in class org.jmol.script.ScriptVariable
getVariableMap(Object) - Static method in class org.jmol.script.ScriptVariable
getVariableNames() - Method in interface etomica.graph.engine.Environment
getVariableNames() - Method in class etomica.graph.engine.impl.EnvironmentImpl
getVariableValue(String) - Method in interface etomica.graph.engine.Environment
getVariableValue(String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
getVdwLabel() - Method in enum org.jmol.constant.EnumVdw
getVdwType(String) - Static method in enum org.jmol.constant.EnumVdw
getVdwType2(String) - Static method in enum org.jmol.constant.EnumVdw
getVector() - Method in class etomica.math.Quaternion: Returns the vector part of the Quaternion as IVector
getVector(int) - Method in class org.jmol.util.Quaternion
getVectorAsDoubleArray() - Method in class etomica.math.Quaternion: Returns the vector associated with the Quaternion as a double array
getVectorMagnitude() - Method in class etomica.math.Quaternion: Returns the magnitude of the vector associated with the Quaternion
getVectorScale() - Method in class etomica.action.BoxInflate: Returns the current value of the inflation scale in each dimension.
getVectorsFromFile(String) - Static method in class etomica.normalmode.ArrayReader1D
getVectorsFromFile(String) - Static method in class etomica.util.numerical.ArrayReader1D
getVelocity() - Method in interface etomica.api.IAtomKinetic: Returns the velocity of the IAtom.
getVelocity() - Method in class etomica.atom.AtomLeafDynamic
getVelocity() - Method in interface etomica.atom.IMoleculeKinetic
getVelocity() - Method in class etomica.atom.MoleculeOrientedDynamic
getVelocityAverage(IMolecule) - Method in class etomica.atom.AtomGroupVelocityAverage: Returns the mass-average velocity of the given Atom and all its children.
getVertex1() - Method in class g3dsys.images.Triangle
getVertex2() - Method in class g3dsys.images.Triangle
getVertex3() - Method in class g3dsys.images.Triangle
getVertexCount() - Method in class etomica.math.geometry.Polytope: Number of vertices in the polytrope.
getVertexCount(int) - Static method in class org.jmol.util.Geodesic
getVertexVector(int) - Static method in class org.jmol.util.Geodesic
getVertexVectors() - Static method in class org.jmol.util.Geodesic
getVertexVectors() - Static method in class org.jmol.util.Normix
getVertGBC() - Static method in class etomica.graphics.SimulationPanel
getVertices() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
getVertices() - Method in class etomica.math.geometry.Polytope: Returns an array of all vertices of the polytrope.
getVertices() - Method in class org.jmol.util.MeshSurface
getVib0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
getVib0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
getViewSpeciesSelection() - Method in class etomica.virial.GUI.views.AppViewMixtureBuilder
getVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
getVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
getVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
getVirialGraphs() - Method in class etomica.virial.cluster.VirialDiagrams
getVirialGraphs() - Method in class etomica.virial.cluster.VirialDiagramsPT
getVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
getVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
getVirialProfile() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile: Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
getVirialSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
getVirialSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
getVMax() - Method in class etomica.graphics.DisplayScrollingGraph
getVMin() - Method in class etomica.graphics.DisplayScrollingGraph
getVolume() - Method in class etomica.math.geometry.Circle: Returns the volume for the present sphere radius.
getVolume() - Method in class etomica.math.geometry.Cube: Returns edgeLength^3.
getVolume() - Method in class etomica.math.geometry.Cuboid
getVolume() - Method in class etomica.math.geometry.Hypersphere
getVolume() - Method in class etomica.math.geometry.LineSegment
getVolume() - Method in class etomica.math.geometry.Parallelepiped: Calculated parallelepiped volume using (a X b) .
getVolume() - Method in class etomica.math.geometry.Point: Returns zero.
getVolume() - Method in class etomica.math.geometry.Polygon: Returns the 2-D volume of the polygon, which is its area
getVolume() - Method in class etomica.math.geometry.PolyhedronGeneral: Returns the 3-D volume of the polyhedron, which is its conventional volume
getVolume() - Method in class etomica.math.geometry.Polytope: Returns the (hyper)volume enclosed by the polytope.
getVolume() - Method in interface etomica.math.geometry.Shape: Returns the (hyper-)volume of the enclosed region.
getVolume() - Method in class etomica.math.geometry.Sphere: Returns the volume for the present sphere radius.
getVolume() - Method in class etomica.math.geometry.TruncatedOctahedron
getVSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff: Returns the current value of the energy sum.
getVZero() - Method in class etomica.yukawa.P2Yukawa
getW() - Method in class etomica.freeenergy.npath.P1ImageHarmonic
getW(int) - Method in class etomica.virial.cluster.ClusterOperations: Returns all diagrams of order n in the sum [eta(r) + b(r)] (i.e., the sum of the indirect correlation function and the bridge function).
getWallDim() - Method in class etomica.modules.dcvgcmd.P1WCAWall
getWallDim() - Method in class etomica.modules.sam.P1WCAWall
getWallForce() - Method in interface etomica.modules.rosmosis.IPotentialCalculationWallForce
getWallForce() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
getWallForce() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
getWallForce() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
getWallPosition() - Method in class etomica.modules.sam.P1WCAWall
getWallPosition() - Method in class etomica.nbr.CriterionPositionWall: Returns the position of the wall.
getWallPosition() - Method in class etomica.potential.P1HardMovingBoundary
getWallPositionDimension() - Method in class etomica.nbr.CriterionPositionWall
getWallPositionDimension() - Method in class etomica.potential.P1HardMovingBoundary
getWallPotential() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
getWallVelocity() - Method in class etomica.potential.P1HardMovingBoundary
getWallVelocityDimension() - Method in class etomica.potential.P1HardMovingBoundary
getWaveVectorFactory() - Method in class etomica.normalmode.CalcJacobian
getWaveVectorFactory() - Method in class etomica.normalmode.LatticeSumMolecularCrystal
getWaveVectorFactory() - Method in class etomica.normalmode.MeterNormalMode
getWaveVectorFactory() - Method in interface etomica.normalmode.NormalModes: Returns a factory that provides the wave vectors and coefficients for the periodic system.
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModes1DHR
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModes2D
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModes3D
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesFromFile
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesMolecular
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesPotential
getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesSoftSpherical
getWaveVectorFactory() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
getWaveVectorNum() - Method in class etomica.normalmode.DeviceWaveVectorSlider
getWaveVectorNum() - Method in class etomica.normalmode.IntegratorHarmonic
getWaveVectors() - Method in class etomica.normalmode.IntegratorHarmonic
getWaveVectors() - Method in class etomica.normalmode.MeterNormalMode
getWaveVectors() - Method in class etomica.normalmode.NormalModesVariable
getWaveVectors() - Method in interface etomica.normalmode.WaveVectorFactory: Returns the wave vectors generated by makeWaveVectors
getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactory1D
getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactory2D
getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactoryFcc
getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactoryFromFile
getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactorySimple
getWeight() - Method in class etomica.virial.cluster.ClusterDiagram
getWeightCoefficients() - Method in class etomica.virial.ClusterWeightUmbrella
getWeights() - Method in class etomica.virial.ClusterSum
getWeightUpdateInterval() - Method in class etomica.tmmc.IntegratorTMMC: Accessor method for number of doStep calls between updating of weights.
getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationCone: Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for attractive-well diameter divided by sigma
getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationCone
getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
getWellDiameter() - Method in class etomica.potential.P2HardAssociation: Accessor for well diameter.
getWellDiameterDimension() - Method in class etomica.potential.P2HardAssociation
getWellEdgeCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
getWellEpsilon() - Method in class etomica.potential.P2HardAssociationCone: Accessor method for attractive-well depth parameter.
getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for attractive-well depth parameter.
getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for attractive-well depth parameter.
getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for attractive-well depth parameter.
getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for attractive-well depth parameter.
getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for attractive-well depth parameter.
getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationCone
getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
getWidth() - Method in class etomica.graph.view.rasterizer.SVGConverter
getWindow(Container) - Static method in class org.jmol.awt.Platform
getWrappedCriterion() - Method in class etomica.nbr.CriterionAdapter: Returns the criterion wrapped by this adapter
getWrappedCriterion() - Method in class etomica.nbr.molecule.CriterionAdapterMolecular: Returns the criterion wrapped by this adapter
getWrappedModifier() - Method in class etomica.modifier.ModifyAction
getWrappedPotential() - Method in class etomica.normalmode.P2XOrder
getWrappedPotential() - Method in class etomica.potential.P2HardWrapper
getWrappedPotential() - Method in class etomica.potential.P2MoleculeMonatomic
getWrappedPotential() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched: Returns the wrapped potential.
getWrappedPotential() - Method in class etomica.potential.P2MoleculeTruncated: Returns the wrapped potential.
getWrappedPotential() - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the wrapped potential.
getWrappedPotential() - Method in class etomica.potential.P2SoftSphericalTruncatedShifted: Returns the wrapped potential.
getWrappedPotential() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched: Returns the wrapped potential.
getWrappedPotential() - Method in class etomica.potential.P2SoftTruncated: Returns the wrapped potential.
getWrappedRandom() - Method in class etomica.util.RandomNumberGenerator
getWrapperClass(String) - Method in class etomica.util.ReadParameters
getWriteInterval() - Method in class etomica.data.DataLogger
getWriteOnFinishDataSource() - Method in class etomica.data.DataLogger
getWriteScale() - Method in class etomica.graphics.DisplayCanvas
getWriteVelocity() - Method in class etomica.action.WriteConfigurationDLPOLY
getWriteVelocity() - Method in class etomica.action.WriteConfigurationP2DLPOLY
getX(int) - Method in interface etomica.api.IVector: Vector components corresponding to the given index.
getX(int) - Method in class etomica.space1d.Vector1D
getX(int) - Method in class etomica.space2d.Vector2D
getX(int) - Method in class etomica.space3d.Vector3D
getX(int) - Method in class etomica.spaceNd.VectorND
getX() - Method in class g3dsys.images.Ball
getX() - Method in class g3dsys.images.Ellipse
getX0() - Method in class etomica.mappedvirial.MappedUpotential
getX0() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
getX0() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
getX0() - Method in class etomica.potential.P1Harmonic
getX0Dimension() - Method in class etomica.potential.P1Harmonic
getXCellModifier() - Method in class etomica.normalmode.DeviceCellNumXYSlider
getXCellNum() - Method in class etomica.normalmode.DeviceCellNumXYSlider
getXDataSource() - Method in class etomica.data.meter.MeterDihedralAngle
getXDataSource() - Method in class etomica.data.meter.MeterProfileByVolume
getXDataSource() - Method in class etomica.data.meter.MeterRDF
getXDataSource() - Method in class etomica.data.meter.MeterRDFPC
getXDataSource() - Method in class etomica.data.meter.PotentialCalculationRDF
getXDataSource() - Method in class etomica.data.types.DataFunction.DataInfoFunction
getXDataSource() - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory: Returns a copy of array of independent DataInfo.
getXicom() - Method in class etomica.util.numerical.Function1d
getXMax() - Method in class etomica.data.DataSourceUniform: Accessor method for the right limit of the range.
getXMin() - Method in class etomica.data.DataSourceUniform: Accessor method for the left limit of the range.
getXRange() - Method in interface etomica.util.Histogram: Returns the range of x values (min and max) used in the histogram.
getXRange() - Method in class etomica.util.HistogramDiscrete
getXRange() - Method in class etomica.util.HistogramNotSoSimple
getXRange() - Method in class etomica.util.HistogramReweightedData
getXRange() - Method in class etomica.util.HistogramSimple
getXRot() - Method in class etomica.graphics.DisplayCanvas
getXSource() - Method in class etomica.data.DataSourceFunction: Returns the DataSourceUniform instance that generates the x values.
getXType() - Method in class etomica.models.rowley.SpeciesEthanol
getXType() - Method in class etomica.models.rowley.SpeciesMethanol
getXValues() - Method in interface etomica.util.History: Returns an array containing the x values that have been added to the History.
getXValues() - Method in class etomica.util.HistoryCollapsing
getXValues() - Method in class etomica.util.HistoryComplete
getXValues() - Method in class etomica.util.HistoryScrolling
getXzOrientationTensor() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
getY() - Method in class g3dsys.images.Ball
getY() - Method in class g3dsys.images.Ellipse
getYCellModifier() - Method in class etomica.normalmode.DeviceCellNumXYSlider
getYCellNum() - Method in class etomica.normalmode.DeviceCellNumXYSlider
getYesButton() - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
getyOrientationTensor() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
getYRot() - Method in class etomica.graphics.DisplayCanvas
getYScale() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
getZ() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
getZ() - Method in class g3dsys.images.Ball
getZ() - Method in class g3dsys.images.Ellipse
getZ1() - Method in class etomica.potential.P2ModifiedMorse
getZ2() - Method in class etomica.potential.P2ModifiedMorse
getZero() - Method in class etomica.veos.BigValue
getZero() - Method in interface etomica.veos.IBigValue: Returns an instance of the class representing the value zero.
getZero() - Method in class etomica.veos.MyBigDecimal
getZFraction() - Method in class etomica.modules.adsorption.MyMCMove
getZFraction() - Method in class etomica.modules.dcvgcmd.MyMCMove: Returns the zFraction.
getZoom() - Method in class etomica.graphics.DisplayCanvas
ghostBox - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
ghostBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
ghostBox - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
gi - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
gi - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
gi - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
gi - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
GIGA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺⁹.
gjke(AtomOrientedQuaternion, AtomOrientedQuaternion) - Method in class etomica.potential.P2SpheroPolyhedron
globalAtomIndexChanged(int) - Method in class etomica.box.BoxEventManager
globalAtomLeafIndexChanged(int) - Method in class etomica.box.BoxEventManager
GlobalFilter - Class in etomica.graph.iterators.filters: A GlobalFilter is one that must see the entire graph stream before returning any graph.
GlobalFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.GlobalFilter
GlobalFilter(GraphIterator, GlobalFilter.SignatureMaker) - Constructor for class etomica.graph.iterators.filters.GlobalFilter
GlobalFilter.SignatureMaker - Class in etomica.graph.iterators.filters
globalMoveProbability - Variable in class etomica.integrator.IntegratorManagerMC
go() - Method in class etomica.util.numerical.AkimaSplineSmootherApp
go() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp
goButton - Variable in class etomica.modules.clustergenerator.MyApplet
goFastButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
GOLD - Static variable in class org.jmol.util.Colix
Gperp - Variable in class etomica.dimer.IntegratorDimerRT
Gperplast - Variable in class etomica.dimer.IntegratorDimerRT
Gpol - Variable in class etomica.models.water.P2WaterSzalewicz
Grabber - Class in etomica.util
Grabber(String) - Constructor for class etomica.util.Grabber
grabber - Variable in class etomica.util.Grabber.ActionCornerSetter
grabber - Variable in class etomica.util.Grabber.CornerSetListener
grabber - Variable in class etomica.util.Grabber.DefaultMouseListener
Grabber.ActionCornerSetter - Class in etomica.util
Grabber.CornerData - Class in etomica.util
Grabber.CornerSetListener - Class in etomica.util
Grabber.DefaultMouseListener - Class in etomica.util
Grabber.ImagePanel - Class in etomica.util
grabPixels(Object, int, int, int[], int, int) - Method in interface org.jmol.api.ApiPlatform
grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awt.Platform
grad - Variable in class etomica.interfacial.P1Wall
gradient(IAtomList) - Method in class etomica.dimer.P1LepsHarmonic
gradient(IAtomList, Tensor) - Method in class etomica.dimer.P1LepsHarmonic
gradient - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
gradient(IAtomList) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
gradient(IAtomList, Tensor) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
gradient(IAtomList) - Method in class etomica.interfacial.P1Wall
gradient(IAtomList, Tensor) - Method in class etomica.interfacial.P1Wall
gradient - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
gradient(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti: Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList, Tensor) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
gradient - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
gradient(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat: Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList, Tensor) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
gradient - Variable in class etomica.meam.PotentialCuLREP
gradient(IAtomList) - Method in class etomica.meam.PotentialCuLREP
gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialCuLREP
gradient - Variable in class etomica.meam.PotentialEFS
gradient(IAtomList) - Method in class etomica.meam.PotentialEFS
gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialEFS
gradient - Variable in class etomica.meam.PotentialFeEAM
gradient(IAtomList) - Method in class etomica.meam.PotentialFeEAM
gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialFeEAM
gradient - Variable in class etomica.meam.PotentialFeEAM_LS
gradient(IAtomList) - Method in class etomica.meam.PotentialFeEAM_LS
gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialFeEAM_LS
gradient(IAtomList) - Method in class etomica.meam.PotentialMEAM
gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialMEAM
gradient(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
gradient(IAtomList, Tensor) - Method in class etomica.models.co2.P2CO2H2OWheatley
gradient(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
gradient(IAtomList, Tensor) - Method in class etomica.models.co2.P2CO2Hellmann
gradient - Variable in class etomica.models.nitrogen.P2Nitrogen
gradient(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
gradient(IMoleculeList, Tensor) - Method in class etomica.models.nitrogen.P2Nitrogen
gradient - Variable in class etomica.models.nitrogen.P2NitrogenAB
gradient(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenAB
gradient(IMoleculeList, Tensor) - Method in class etomica.models.nitrogen.P2NitrogenAB
gradient - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
gradient(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
gradient(IMoleculeList, Tensor) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
gradient - Variable in class etomica.models.water.P2Water3PSoft
gradient(IMoleculeList) - Method in class etomica.models.water.P2Water3PSoft
gradient(IMoleculeList, Tensor) - Method in class etomica.models.water.P2Water3PSoft
gradient - Variable in class etomica.models.water.P2Water4PSoft
gradient(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
gradient(IMoleculeList, Tensor) - Method in class etomica.models.water.P2Water4PSoft
gradient(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
gradient(IAtomList, Tensor) - Method in class etomica.models.water.P2WaterSzalewicz
gradient(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
gradient(IAtomList, Tensor) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
gradient - Variable in class etomica.modules.dcvgcmd.P1WCAWall
gradient(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
gradient(IAtomList, Tensor) - Method in class etomica.modules.dcvgcmd.P1WCAWall
gradient - Variable in class etomica.modules.droplet.P1Smash
gradient(IAtomList, Tensor) - Method in class etomica.modules.droplet.P1Smash
gradient(IAtomList) - Method in class etomica.modules.droplet.P1Smash
gradient(IAtomList, Tensor) - Method in class etomica.modules.droplet.P2Cohesion
gradient(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
gradient(IAtomList, Tensor) - Method in class etomica.modules.materialfracture.P1Tension
gradient(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
gradient - Variable in class etomica.modules.rosmosis.P1Tether
gradient(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
gradient(IAtomList, Tensor) - Method in class etomica.modules.rosmosis.P1Tether
gradient - Variable in class etomica.modules.sam.P1Sinusoidal
gradient(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
gradient(IAtomList, Tensor) - Method in class etomica.modules.sam.P1Sinusoidal
gradient - Variable in class etomica.modules.sam.P1WCAWall
gradient(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
gradient(IAtomList, Tensor) - Method in class etomica.modules.sam.P1WCAWall
gradient(IAtomList) - Method in class etomica.paracetamol.P2ElectrostaticDreiding
gradient - Variable in class etomica.potential.EwaldSummation
gradient(IAtomList) - Method in class etomica.potential.EwaldSummation
gradient(IAtomList, Tensor) - Method in class etomica.potential.EwaldSummation
gradient(IAtomList) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
gradient(IAtomList, Tensor) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
gradient(IAtomList) - Method in class etomica.potential.P1Harmonic
gradient(IAtomList, Tensor) - Method in class etomica.potential.P1Harmonic
gradient(IAtomList) - Method in class etomica.potential.P1HarmonicSite
gradient(IAtomList, Tensor) - Method in class etomica.potential.P1HarmonicSite
gradient(IAtomList) - Method in class etomica.potential.P1SoftBoundary
gradient(IAtomList, Tensor) - Method in class etomica.potential.P1SoftBoundary
gradient(IAtomList) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
gradient(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSites
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2HardAssociationConeFourSites
gradient(IAtomList) - Method in class etomica.potential.P2HardAssociationConeOneSite
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2HardAssociationConeOneSite
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2HSDipole
gradient(IMoleculeList) - Method in class etomica.potential.P2HSDipole
gradient(IAtomList) - Method in class etomica.potential.P2Ideal: Returns a zero vector.
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2Ideal
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2LJDipole
gradient(IMoleculeList) - Method in class etomica.potential.P2LJDipole
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2LJQ
gradient(IAtomList) - Method in class etomica.potential.P2LJQ
gradient(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
gradient(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2NitrogenHellmann
gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipole
gradient - Variable in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
gradient - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
gradient(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
gradient - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
gradient(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
gradient - Variable in class etomica.potential.P2SoftTruncated
gradient(IAtomList) - Method in class etomica.potential.P2SoftTruncated: Returns the derivative (r du/dr) of the wrapped potential if the separation is less than the cutoff value
gradient(IAtomList, Tensor) - Method in class etomica.potential.P2SoftTruncated: Returns the derivative (r du/dr) of the wrapped potential if the separation is less than the cutoff value
gradient - Variable in class etomica.potential.P3BondAngle
gradient(IAtomList) - Method in class etomica.potential.P3BondAngle
gradient(IAtomList, Tensor) - Method in class etomica.potential.P3BondAngle
gradient - Variable in class etomica.potential.P3BondAngleDreiding
gradient(IAtomList, Tensor) - Method in class etomica.potential.P3BondAngleDreiding
gradient(IAtomList) - Method in class etomica.potential.P3BondAngleDreiding
gradient - Variable in class etomica.potential.P3CPSNonAdditiveHe
gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHe
gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHe
gradient - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
gradient - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
gradient - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
gradient - Variable in class etomica.potential.P4BondTorsion
gradient(IAtomList) - Method in class etomica.potential.P4BondTorsion
gradient(IAtomList, Tensor) - Method in class etomica.potential.P4BondTorsion
gradient - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
gradient(IAtomList) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
gradient(IAtomList, Tensor) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
gradient(IAtomList, Tensor) - Method in class etomica.potential.P4BondTorsionOPLS
gradient - Variable in class etomica.potential.P4TorsionDreiding
gradient(IAtomList, Tensor) - Method in class etomica.potential.P4TorsionDreiding
gradient(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
gradient - Variable in class etomica.potential.Potential2SoftSpherical
gradient(IAtomList) - Method in class etomica.potential.Potential2SoftSpherical: Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList, Tensor) - Method in class etomica.potential.Potential2SoftSpherical
gradient - Variable in class etomica.potential.Potential2SoftSphericalLS
gradient(IAtomList) - Method in class etomica.potential.Potential2SoftSphericalLS: Gradient of the pair potential as given by the du(double) method.
gradient(IAtomList, Tensor) - Method in class etomica.potential.Potential2SoftSphericalLS
gradient(IMoleculeList) - Method in class etomica.potential.PotentialGroupSoft
gradient(IMoleculeList, Tensor) - Method in class etomica.potential.PotentialGroupSoft
gradient(IMoleculeList) - Method in interface etomica.potential.PotentialMolecularSoft: Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied.
gradient(IMoleculeList, Tensor) - Method in interface etomica.potential.PotentialMolecularSoft: Returns the same gradient as gradient(IMoleculeList) and also adds in the contribution of the molecules to the pressureTensor.
gradient(IAtomList) - Method in interface etomica.potential.PotentialSoft: Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied.
gradient(IAtomList, Tensor) - Method in interface etomica.potential.PotentialSoft: Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor.
gradient(IMoleculeList, Tensor) - Method in class etomica.rotation.P2LJDipole
gradient(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
gradient2 - Variable in class etomica.potential.EwaldSummation.P2EwaldReal
gradientAndTorque - Variable in class etomica.models.co2.P2CO2H2OWheatley
gradientAndTorque(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
gradientAndTorque - Variable in class etomica.models.co2.P2CO2Hellmann
gradientAndTorque(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
gradientAndTorque - Variable in class etomica.models.nitrogen.P2Nitrogen
gradientAndTorque(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
gradientAndTorque - Variable in class etomica.models.water.P2Water3PSoft
gradientAndTorque(IMoleculeList) - Method in class etomica.models.water.P2Water3PSoft
gradientAndTorque - Variable in class etomica.models.water.P2Water4PSoft
gradientAndTorque(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
gradientAndTorque(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
gradientAndTorque(IMoleculeList) - Method in interface etomica.potential.IPotentialMolecularTorque
gradientAndTorque(IAtomList) - Method in interface etomica.potential.IPotentialTorque
gradientAndTorque - Variable in class etomica.potential.P2HSDipole
gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2HSDipole
gradientAndTorque - Variable in class etomica.potential.P2LJDipole
gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2LJDipole
gradientAndTorque - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
gradientAndTorque - Variable in class etomica.potential.P2NitrogenHellmann
gradientAndTorque(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
gradientAndTorque - Variable in class etomica.potential.P2ReactionFieldDipole
gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
gradientAndTorque - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
gradientAndTorque - Variable in class etomica.rotation.P2LJDipole
gradientAndTorque(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
gradients - Variable in class etomica.potential.PotentialGroupSoft
GraftAction(int) - Constructor for class etomica.modules.colloid.ColloidGraphic.GraftAction
graftVectors - Variable in class etomica.modules.colloid.ConfigurationColloid
GrainBoundaryConfiguration - Class in etomica.config
GrainBoundaryConfiguration(BravaisLatticeCrystal, BravaisLatticeCrystal, ISpace) - Constructor for class etomica.config.GrainBoundaryConfiguration: Construct class that will place atoms on sites of the given lattices, proceeding in the order resulting from iteration through the given index iterator.
GrainBoundaryTiltConfiguration - Class in etomica.config
GrainBoundaryTiltConfiguration(BravaisLatticeCrystal, BravaisLatticeCrystal, ISpecies[], double, ISpace) - Constructor for class etomica.config.GrainBoundaryTiltConfiguration
Gram - Class in etomica.units
Graph - Interface in etomica.graph.model
GraphExtract - Class in etomica.graph.operations: This class takes the given nodes from the given graph and returns a new graph consisting only of those nodes (and the bonds between them).
GraphExtract() - Constructor for class etomica.graph.operations.GraphExtract
GraphFactory - Class in etomica.graph.model
GraphFactory() - Constructor for class etomica.graph.model.GraphFactory
graphHasEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2Site
graphHasEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2SiteRho
graphHasEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
graphHasEdgeColor(Graph, char) - Static method in class etomica.virial.cluster.VirialDiagrams
graphHasEdgeColor(Graph, char) - Static method in class etomica.virial.cluster.VirialDiagramsMix2
graphHasEdgeColor(Graph, char) - Static method in class etomica.virial.cluster.VirialDiagramsPT
graphic() - Method in class etomica.graphics.DefaultToolbar
graphic(Object) - Method in class etomica.graphics.Device
graphic() - Method in class etomica.graphics.Device: Same as graphic method with a null argument.
graphic(Object) - Method in class etomica.graphics.DeviceBox
graphic(Object) - Method in class etomica.graphics.DeviceButton: Returns the GUI element for display in the simulation.
graphic(Object) - Method in class etomica.graphics.DeviceButtonGroup
graphic(Object) - Method in class etomica.graphics.DeviceCheckBox: Returns the GUI box element for display in the simulation.
graphic() - Method in class etomica.graphics.DeviceDelaySlider
graphic() - Method in class etomica.graphics.DevicePlotPoints: Returns the top level panel that the function plot components sit on.
graphic(Object) - Method in class etomica.graphics.DeviceSelector: Returns the GUI element for display in the simulation.
graphic(Object) - Method in class etomica.graphics.DeviceSlider: Returns the GUI element for display in the simulation.
graphic(Object) - Method in class etomica.graphics.DeviceSpinner: Returns the GUI element for display in the simulation.
graphic(Object) - Method in class etomica.graphics.DeviceTable: Returns the top level panel that the table components sit on.
graphic(Object) - Method in class etomica.graphics.DeviceTernarySelector: Graphical display given by this device.
graphic(Object) - Method in class etomica.graphics.DeviceThermoSelector: Returns the GUI element for display in the simulation.
graphic(Object) - Method in class etomica.graphics.DeviceThermoSlider
graphic(Object) - Method in class etomica.graphics.DeviceToggleRadioButtons: Returns the GUI button element for display in the simulation.
graphic(Object) - Method in class etomica.graphics.DeviceTrioControllerButton: Returns the JPanel that contains the buttons.
graphic(Object) - Method in class etomica.graphics.Display: Method of Simulation.GraphicElement interface.
graphic() - Method in class etomica.graphics.Display: Same as graphic method with a null argument.
graphic(Object) - Method in class etomica.graphics.DisplayBox: Simulation.GraphicalElement interface method.
graphic(Object) - Method in class etomica.graphics.DisplayPlot: Overrides superclass method to return a JPanel holding the plot.
graphic(Object) - Method in class etomica.graphics.DisplayPolytope: Simulation.GraphicalElement interface method.
graphic(Object) - Method in class etomica.graphics.DisplayTable
graphic(Object) - Method in class etomica.graphics.DisplayTextBox
graphic(Object) - Method in class etomica.graphics.DisplayTextBoxesCAE
graphic(Object) - Method in interface etomica.graphics.GraphicalElement: Interface for a Simulation element that would be used in a simulation graphical user interface (GUI)
graphic - Variable in class etomica.modules.droplet.EllipseDisplayAction
graphic() - Method in class etomica.modules.osmosis.Osmosis.InitializeMolecules
graphic(Object) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
graphic(Object) - Method in class etomica.normalmode.DeviceCellNum3DSlider
graphic(Object) - Method in class etomica.normalmode.DeviceCellNumXYSlider
graphic(Object) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
graphic(Object) - Method in class etomica.normalmode.DeviceWaveVectorSlider
graphic(Object) - Method in class etomica.zeolite.DeviceButtonSingle: Returns the GUI element for display in the simulation.
GRAPHIC_ONLY - Static variable in class etomica.graphics.SimulationGraphic
GraphicalElement - Interface in etomica.graphics: Interface for a simulation element that can make a graphical component
graphicOut - Variable in class etomica.modules.clustergenerator.MyApplet
graphicOut2 - Variable in class etomica.modules.clustergenerator.MyApplet
graphics - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
graphics - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
graphics - Variable in class etomica.interfacial.LJMC.LjMC3DParams
graphics - Variable in class etomica.interfacial.LJMD.LJMDParams
graphics - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
graphics - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
graphics - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
graphics - Variable in class etomica.mappedvirial.MappedU.LJMDParams
graphics - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
graphics - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
graphics - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
graphics - Variable in class etomica.normalmode.SimLJVacancy.LJParams
graphics - Static variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
graphics - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
graphics - Static variable in class etomica.virial.simulations.VirialTraPPEAlcohol
Graphics3D - Class in org.jmol.g3d: Provides high-level graphics primitives for 3D visualization for the software renderers.
Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
graphicsForMetrics - Variable in class org.jmol.util.GData
graphicsPanel - Variable in class etomica.graphics.SimulationPanel
graphicsToggler - Variable in class etomica.modules.clustergenerator.MyApplet
GraphicsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.GraphicsToggler
GraphImpl - Class in etomica.graph.model.impl
GraphImpl(Node[]) - Constructor for class etomica.graph.model.impl.GraphImpl
GraphImpl(byte) - Constructor for class etomica.graph.model.impl.GraphImpl
GraphImpl(byte, byte) - Constructor for class etomica.graph.model.impl.GraphImpl
GraphImpl(byte, Bitmap) - Constructor for class etomica.graph.model.impl.GraphImpl
GraphImpl(byte, byte, Bitmap) - Constructor for class etomica.graph.model.impl.GraphImpl
GraphImpl(byte, byte, Bitmap, Coefficient) - Constructor for class etomica.graph.model.impl.GraphImpl
GraphIterator - Interface in etomica.graph.model
GraphList<E> - Class in etomica.graph.model
GraphList() - Constructor for class etomica.graph.model.GraphList
GraphList(Comparator<E>) - Constructor for class etomica.graph.model.GraphList
GraphMap - Class in etomica.graph.viewer
GraphMap(Set<Graph>, JComponent) - Constructor for class etomica.graph.viewer.GraphMap
GraphNumber - Class in etomica.graph.util
GraphNumber() - Constructor for class etomica.graph.util.GraphNumber
GraphOp - Interface in etomica.graph.operations: Interface for a simple operation that takes a Graph and returns a Graph.
graphOp - Variable in class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
GraphOp.GraphOpNull - Class in etomica.graph.operations: A dummy implementation of GraphOp that does nothing.
GraphOpMaxRoot - Class in etomica.graph.operations: GraphOp class that adjusts root points in each component so that + the number of root points is maintained + no component has more than one root point + all root points are included in all the "earliest" components + if a component has a root point, it is the first node in that component This class only makes sense if the specific identity of each root point is unimportant (Metadata.ROOT_POINTS_SPECIAL=false).
GraphOpMaxRoot() - Constructor for class etomica.graph.operations.GraphOpMaxRoot
GraphOpNull() - Constructor for class etomica.graph.operations.GraphOp.GraphOpNull
graphs - Static variable in class etomica.graph.isomorphism.Match
graphSegment - Variable in class etomica.graph.property.FFTDecomposition
graphSplitter - Variable in class etomica.graph.operations.Unfactor
GRAY - Static variable in class org.jmol.util.Colix
GREATER_THAN - Static variable in class etomica.compatibility.Feature
GREEN - Static variable in class org.jmol.util.Colix
greenLight - Variable in class etomica.threaded.atom.PotentialMasterListWorker
greenLight - Variable in class etomica.threaded.domain.PotentialMasterListWorker
greys - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
greyscalerendering - Static variable in class org.jmol.script.Token
group - Static variable in class org.jmol.script.Token
group1 - Static variable in class org.jmol.script.Token
groupid - Static variable in class org.jmol.script.Token
GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_ARGININE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_LYSINE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_PROLINE - Static variable in class org.jmol.viewer.JmolConstants
GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JmolConstants
groupindex - Static variable in class org.jmol.script.Token
groupScaler - Variable in class etomica.action.BoxInflate
groupStart - Static variable in class etomica.virial.cluster.VirialDiagrams
groupTag - Variable in class etomica.normalmode.MeterTiltRotationHistogram
groupTranslationVector - Variable in class etomica.association.BiasVolume2SiteAceticAcid
groupTranslationVector - Variable in class etomica.association.BiasVolumeAceticAcid
groupTranslationVector - Variable in class etomica.association.MCMoveBiasUBMolecule
groupTranslationVector - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
groupTranslationVector - Variable in class etomica.integrator.mcmove.MCMoveMolecule
groupTransVect - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
groupTransVect - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
groupTransVect - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
groupTransVect - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
growMolecule - Variable in class etomica.models.hexane.TestHexane
growMolecule - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
growMolecule - Variable in class etomica.models.hexane.TestHexaneFileConfig
growMolecule - Variable in class etomica.models.hexane.TestSetToUHexane
growto(BigInteger) - Method in class etomica.veos.bigdecimal.Prime: extend the list of known primes up to n
gruneisen_knu - Variable in class etomica.normalmode.MeterSolidPropsLJ
gSat - Variable in class etomica.interfacial.P1Wall
gScaled - Variable in class org.jmol.util.Rgb16
gSet1 - Variable in class etomica.graph.operations.UnaryChain
GSTAR - Variable in class etomica.math.Gamma
gSum - Variable in class etomica.data.meter.MeterDihedralAngle
gSum - Variable in class etomica.data.meter.MeterRDF
gSum - Variable in class etomica.data.meter.PotentialCalculationRDF
gtmp - Variable in class etomica.potential.P4BondTorsion
gtmp - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH

H

h - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
h - Variable in class etomica.util.numerical.FiniteDifferenceDerivative
h - Variable in class etomica.virial.ClusterPY
H1DBO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
H1O - Variable in class etomica.models.water.P2WaterSzalewicz
H1O2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
H1O2 - Variable in class etomica.association.BiasVolumeAceticAcid
H1pol - Static variable in class etomica.models.water.P2WaterSzalewicz
H1SBO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
H2O - Variable in class etomica.models.water.P2WaterSzalewicz
H2O1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
H2O1 - Variable in class etomica.association.BiasVolumeAceticAcid
H2pol - Static variable in class etomica.models.water.P2WaterSzalewicz
hackedup - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
hackedup - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
HALF - Static variable in class etomica.veos.bigdecimal.Rational: The constant 1/2
half_bondlength - Static variable in class etomica.virial.ConformationPh3site
HALF_STEP - Static variable in class etomica.data.DataSourceUniform.LimitType: Limit type indicating that extreme value should be one half step from the specified limit.
halfL - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
halfNeighborCount - Variable in class etomica.lattice.RectangularLatticeNbrIteratorSquare
halfofthebondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
halfUnitCellLength - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
halo - Static variable in class org.jmol.script.Token
halt() - Method in class etomica.action.activity.ActivityGroupParallel
halt() - Method in class etomica.action.activity.ActivityGroupSeries: Request that the activity group terminate its thread as soon as possible.
halt() - Method in class etomica.action.Activity: Request that the activity terminate as soon as safely possible.
HALTED - Static variable in class etomica.action.activity.ControllerEvent
haltRequested - Variable in class etomica.action.Activity
handleGraph(String, byte, GraphList<Graph>) - Static method in class etomica.graph.util.GraphNumber
handleNewAtomNbr(IAtom, AtomLeafAgentManager<AtomArrayList>, NeighborListManager, AtomArrayList) - Method in class etomica.potential.P2SquareWellRobust
handleNewAtomNoNbr(IAtom, AtomLeafAgentManager<AtomArrayList>, IAtomList, AtomArrayList) - Method in class etomica.potential.P2SquareWellRobust
handleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.AbstractOptionHandler
handleOption(String, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.ColorOptionHandler
handleOption(Color, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.ColorOptionHandler
handleOption(String, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.FloatOptionHandler
handleOption(float, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.FloatOptionHandler
handleOption(SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
handleOption(String[], SVGConverter) - Method in interface etomica.graph.view.rasterizer.Main.OptionHandler: The OptionHandler should configure the SVGConverter according to the value of the option.
handleOption(String, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
handleOption(Rectangle2D, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
handleOption(String, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
handleOption(String, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.TimeOptionHandler
handleOption(float, SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.TimeOptionHandler
handlingEvent - Variable in class etomica.integrator.IntegratorHard
hankelSymb(Rational, int) - Static method in class etomica.veos.bigdecimal.Rational: Hankel's symbol (n,k)
hap - Variable in class etomica.graph.operations.Factor
hap - Variable in class etomica.graph.operations.FactorOnce
hap - Variable in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
hap - Variable in class etomica.virial.cluster.VirialDiagramsMix2.MaxIsomorphCriteriaMixture
hap - Variable in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
har2kcal - Static variable in class etomica.potential.P2WaterPotentialsJankowski
hardCore - Variable in class etomica.models.water.P2WaterTIP4PHardCore
HardRods - Class in etomica.veos
HardRods() - Constructor for class etomica.veos.HardRods
HardRods(int) - Constructor for class etomica.veos.HardRods
HardSphere - Class in etomica.statmech: Hard sphere properties based on the Hall EOS.
HardSphere() - Constructor for class etomica.statmech.HardSphere
HardSphereFluid - Class in etomica.statmech: Computes EOS for HS fluid.
HardSphereFluid() - Constructor for class etomica.statmech.HardSphereFluid
HardSphereSolid - Class in etomica.statmech: Hard sphere solid EOS.
HardSphereSolid() - Constructor for class etomica.statmech.HardSphereSolid
HardSphereSolid.EOSParams - Class in etomica.statmech
Harmonic - Class in etomica.veos.bigdecimal: Harmonic numbers.
Harmonic() - Constructor for class etomica.veos.bigdecimal.Harmonic: ctor() Does nothing.
HarmonicAlphaNitrogenModel - Class in etomica.models.nitrogen
HarmonicAlphaNitrogenModel(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
HarmonicAlphaNitrogenModelDecomposed - Class in etomica.models.nitrogen: Class that constructs the Hessian Matrix Special features about this class is that: 1.
HarmonicAlphaNitrogenModelDecomposed(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
HarmonicAlphaNitrogenModelLatticeSum - Class in etomica.models.nitrogen: Lattice sum class for Alpha-phase Nitrogen
HarmonicAlphaNitrogenModelLatticeSum(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelLatticeSum
HarmonicAlphaNitrogenModelPairMolecule - Class in etomica.models.nitrogen
HarmonicAlphaNitrogenModelPairMolecule(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
HarmonicAlphaNitrogenModelPairMoleculeSequential - Class in etomica.models.nitrogen: This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction.
HarmonicAlphaNitrogenModelPairMoleculeSequential(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2 - Class in etomica.models.nitrogen: This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction.
HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS - Class in etomica.models.nitrogen: This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction.
HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
HarmonicAlphaNitrogenModelPairMoleculeSequentialLS - Class in etomica.models.nitrogen: This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction.
HarmonicAlphaNitrogenModelPairMoleculeSequentialLS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
HarmonicBetaNitrogenModel - Class in etomica.models.nitrogen: Beta-phase Nitrogen Harmonic Approximation with only 3 translational degrees of freedom
HarmonicBetaNitrogenModel(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModel
HarmonicBetaNitrogenModelDecomposed - Class in etomica.models.nitrogen: Class that constructs the Hessian Matrix Special features about this class is that: 1.
HarmonicBetaNitrogenModelDecomposed(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
HarmonicBetaNitrogenModelLatticeSum - Class in etomica.models.nitrogen: Lattice sum class for Beta-phase Nitrogen
HarmonicBetaNitrogenModelLatticeSum(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelLatticeSum
HarmonicBetaNitrogenModelPairMoleculeSequential - Class in etomica.models.nitrogen: Beta-phase Nitrogen Harmonic Approximation with only 3 translational degrees of freedom
HarmonicBetaNitrogenModelPairMoleculeSequential(ISpace, int, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS - Class in etomica.models.nitrogen: Beta-phase Nitrogen Harmonic Approximation with only 5 degrees of freedom with lattice sum
HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2 - Class in etomica.models.nitrogen: Beta-phase Nitrogen Harmonic Approximation with only 3 translational degrees of freedom
HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2(ISpace, int, String) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS - Class in etomica.models.nitrogen: Beta-phase Nitrogen Harmonic Approximation with only 3 translational degrees of freedom with lattice sum
HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
HarmonicBetaNitrogenModelPairMoleculeSequentialLS - Class in etomica.models.nitrogen: Beta-phase Nitrogen Harmonic Approximation with only 3 translational degrees of freedom with lattice sum
HarmonicBetaNitrogenModelPairMoleculeSequentialLS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
HarmonicCrystal - Class in etomica.normalmode: Properties of a system of monatomic molecules occupying a lattice and interacting according to a spherically-symmetric pair potential.
HarmonicCrystal(double, int[], Primitive, Basis, Potential2SoftSpherical, ISpace) - Constructor for class etomica.normalmode.HarmonicCrystal
HarmonicCrystalMonoclinic - Class in etomica.paracetamol: Properties of a system of monatomic molecules occupying a lattice and interacting according to a spherically-symmetric pair potential.
HarmonicCrystalMonoclinic(int[], Primitive, Basis, IBox, ISpace) - Constructor for class etomica.paracetamol.HarmonicCrystalMonoclinic
HarmonicCrystalOrthorhombic - Class in etomica.paracetamol: Properties of a system of monatomic molecules occupying a lattice and interacting according to a spherically-symmetric pair potential.
HarmonicCrystalOrthorhombic(int[], Primitive, Basis, IBox, CoordinateDefinitionParacetamol, ISpace) - Constructor for class etomica.paracetamol.HarmonicCrystalOrthorhombic
HarmonicCrystalOrthorhombic.LatticeEnergy - Class in etomica.paracetamol
HarmonicCrystalSoftSphereBCC - Class in etomica.normalmode: Properties of a system of monatomic molecules occupying a lattice and interacting according to a soft-sphere spherically-symmetric pair potential.
HarmonicCrystalSoftSphereBCC() - Constructor for class etomica.normalmode.HarmonicCrystalSoftSphereBCC
HarmonicCrystalSoftSphereFCC - Class in etomica.normalmode: Properties of a system of monatomic molecules occupying a lattice and interacting according to a soft-sphere spherically-symmetric pair potential.
HarmonicCrystalSoftSphereFCC() - Constructor for class etomica.normalmode.HarmonicCrystalSoftSphereFCC
HarmonicCrystalSoftSphereHCP - Class in etomica.normalmode: Properties of a system of monatomic molecules occupying a lattice and interacting according to a soft-sphere spherically-symmetric pair potential.
HarmonicCrystalSoftSphereHCP() - Constructor for class etomica.normalmode.HarmonicCrystalSoftSphereHCP
HarmonicCrystalSsFccBigCellNxy - Class in etomica.models.oneDHardRods: Properties of a system of monatomic molecules occupying a lattice and interacting according to a soft-sphere spherically-symmetric pair potential.
HarmonicCrystalSsFccBigCellNxy() - Constructor for class etomica.models.oneDHardRods.HarmonicCrystalSsFccBigCellNxy
HarmonicCrystalSsFccDoubleSize - Class in etomica.models.oneDHardRods: Properties of a system of monatomic molecules occupying a lattice and interacting according to a soft-sphere spherically-symmetric pair potential.
HarmonicCrystalSsFccDoubleSize() - Constructor for class etomica.models.oneDHardRods.HarmonicCrystalSsFccDoubleSize
HarmonicCrystalSsFccNxy - Class in etomica.normalmode: Properties of a system of monatomic molecules occupying a lattice and interacting according to a spherically-symmetric pair potential.
HarmonicCrystalSsFccNxy(int[], Primitive, Basis, Potential2SoftSpherical, ISpace) - Constructor for class etomica.normalmode.HarmonicCrystalSsFccNxy
HarmonicCrystalSsFccNxy.Params - Class in etomica.normalmode
HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS - Class in etomica.models.nitrogen: Disordered alpha-phase This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 3 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction.
HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS - Class in etomica.models.nitrogen: Disordered alpha-phase This class is created to take care of Java out of memory problem when creating a 2D array that is gigantic [~10000][~10000] The class is write a 3 x (nA * dof) Matrix to file while looping through the molecules This class also applied the molecules pair identification algorithm to speed up the matrix construction.
HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
harmonicEnergyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
harmonicEnergyMeter - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
harmonicFudge - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
harmonicFudge - Variable in class etomica.normalmode.NormalModes1DHR
harmonicFudge - Variable in class etomica.normalmode.NormalModes2D
harmonicFudge - Variable in class etomica.normalmode.NormalModes3D
harmonicFudge - Variable in class etomica.normalmode.SimBennet.SimBennetParam
harmonicFudge - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
harmonicFudge - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
harmonicFudge - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
harmonicFudge - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
harmonicStrength - Variable in class etomica.modules.sam.Sam
harmonicWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
Hartree - Class in etomica.units
HasArticulationPair - Class in etomica.graph.property
HasArticulationPair() - Constructor for class etomica.graph.property.HasArticulationPair
HasArticulationPoint - Class in etomica.graph.property
HasArticulationPoint() - Constructor for class etomica.graph.property.HasArticulationPoint
hasContent() - Method in class org.jmol.g3d.Graphics3D
hasEdge(byte) - Method in interface etomica.graph.model.Graph
hasEdge(byte, byte) - Method in interface etomica.graph.model.Graph
hasEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
hasEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
HasEdgeCount - Class in etomica.graph.property
HasEdgeCount(byte) - Constructor for class etomica.graph.property.HasEdgeCount
hasElectrostaticInteraction() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
hasElectrostaticInteraction() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
hasFilter(String) - Method in class etomica.graph.engine.impl.ConstructorImpl
hasFilter(String) - Method in interface etomica.graph.engine.Parser.Constructor
hasFocus(Object) - Method in interface org.jmol.api.ApiPlatform
hasFocus(Object) - Method in class org.jmol.awt.Platform
hashCode() - Method in class etomica.atom.AtomPair
hashCode() - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1).
hashCode() - Method in class etomica.graph.model.impl.BitmapOfLongVector
hashCode() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
hashCode() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
hashCode() - Method in class etomica.virial.IntSet
hashCode() - Method in class org.jmol.util.AxisAngle4f: Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.util.BitSet: Returns a hash code value for this bit set.
hashCode() - Method in class org.jmol.util.Matrix3f: Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.util.Matrix4f: Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.util.Tuple3f: Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.util.Tuple3i: Returns a hash number based on the data values in this object.
hashCode() - Method in class org.jmol.util.Tuple4f: Returns a hash number based on the data values in this object.
HashMapPotentialNonBonded - Class in etomica.virial.GUI.components
hashMapPotentialNonBonded - Variable in class etomica.virial.GUI.components.HashMapPotentialNonBonded
hasNext() - Method in class etomica.atom.AtomLeafAgentManager.AgentIterator
hasNext() - Method in class etomica.atom.AtomTypeAgentManager.AgentIterator
hasNext() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList: Returns true if three non-null atoms have set and a call to reset() has been performed, without any subsequent calls to next() or nextPair().
hasNext() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList: Returns true if three non-null atoms have set and a call to reset() has been performed, without any subsequent calls to next() or nextPair().
hasNext() - Method in class etomica.atom.MoleculeAgentManager.AgentIterator
hasNext() - Method in class etomica.atom.SpeciesAgentManager.AgentIterator
hasNext() - Method in class etomica.box.BoxAgentManager.AgentIterator
hasNext() - Method in class etomica.graph.iterators.CartesianIterator
hasNext() - Method in class etomica.graph.iterators.CartesianPermutator
hasNext() - Method in class etomica.graph.iterators.ChainedIterator
hasNext() - Method in class etomica.graph.iterators.DefaultIterator
hasNext() - Method in class etomica.graph.iterators.DefaultPermutator
hasNext() - Method in class etomica.graph.iterators.EdgelessIterator
hasNext() - Method in class etomica.graph.iterators.filters.GlobalFilter
hasNext() - Method in class etomica.graph.iterators.filters.LocalFilter
hasNext() - Method in class etomica.graph.iterators.FixedEdgeCountIterator
hasNext() - Method in class etomica.graph.iterators.IteratorWrapper
hasNext() - Method in class etomica.graph.iterators.RangePermutator
hasNext() - Method in class etomica.graph.iterators.StoredIterator
hasNext() - Method in interface etomica.lattice.IndexIterator
hasNext() - Method in class etomica.lattice.IndexIteratorRectangular: Indicates whether all iterates have been returned since last call to reset().
hasNext() - Method in class etomica.lattice.IndexIteratorReflecting
hasNext() - Method in class etomica.lattice.IndexIteratorTriangular: Indicates whether prespecified number of iterate have been returned since last call to reset().
hasNext() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
hasNext() - Method in class etomica.lattice.RectangularLattice.Iterator
hasNext() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Indicates whether the iterator has another site.
hasNext() - Method in interface etomica.lattice.SiteIterator: Indicates whether the iterator has another site to return.
hasNext() - Method in class etomica.math.discrete.CombinationIterator
hasNext() - Method in class etomica.math.discrete.PermutationDegenerateIterator
hasNext() - Method in class etomica.math.discrete.PermutationIterator
hasNext() - Method in class etomica.nbr.cell.AtomIteratorCell
hasNext() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
hasNext() - Method in class etomica.virial.PYGenerator.IteratorEF
hasNext() - Method in interface g3dsys.control.IndexIterator: See if there are more indices
hasNextGaussian - Variable in class etomica.util.RandomMersenneTwister
hasNextGaussian - Variable in class etomica.util.RandomNumberGeneratorUnix
HasNodalPoint - Class in etomica.graph.property
HasNodalPoint() - Constructor for class etomica.graph.property.HasNodalPoint
HasNoRootEdge - Class in etomica.graph.property
HasNoRootEdge() - Constructor for class etomica.graph.property.HasNoRootEdge
hasOverflow() - Method in interface etomica.graph.model.Coefficient
hasOverflow() - Method in class etomica.graph.model.impl.CoefficientImpl
hasPBC - Variable in class etomica.normalmode.P2XOrder
hasRowHeaders() - Method in class etomica.data.types.DataTable.DataInfoTable: Returns true if row headers exist.
HasSimpleArticulationPoint - Class in etomica.graph.property: Checks for "simple" articulation points -- ignoring root vs.
HasSimpleArticulationPoint() - Constructor for class etomica.graph.property.HasSimpleArticulationPoint
hasSingleConstructorForPotential(Class) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
hasTarget - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
hasTarget - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
hasUnpushedData - Variable in class etomica.data.DataAccumulator
haveCommon(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
haveQuads - Variable in class org.jmol.util.MeshSurface
haveTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupCoupled
haveTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupExchange
haveTarget(IAtom) - Method in class etomica.atom.iterator.ANIntragroupExchange
haveTarget(IAtom) - Method in class etomica.atom.iterator.ApiIndexList
haveTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntergroup
haveTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntragroup
haveTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasis: Returns true if the given target with the present basis could yield an iterate.
haveTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart: Returns true if the given target with the present basis could yield an iterate.
haveTarget(IAtom) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
haveTarget(IAtom) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
haveTarget(IAtom) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
haveTarget(IAtom) - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent: Returns true if the iterator with its current basis would return an iterate for the given target.
haveTarget(IMolecule) - Method in interface etomica.atom.iterator.MoleculesetIteratorBasisDependent: Returns true if the iterator with its current basis would return an iterate for the given target.
haveTarget(IAtom) - Method in class etomica.atom.iterator.TripletInnerSequential
haveTarget(IAtom) - Method in class etomica.potential.PotentialMaster.AtomIterator0
haveTranslucentObjects() - Method in class org.jmol.g3d.Graphics3D
haveTrueData - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
hbond - Static variable in class org.jmol.script.Token
hbondsangleminimum - Static variable in class org.jmol.script.Token
hbondsbackbone - Static variable in class org.jmol.script.Token
hbondsdistancemaximum - Static variable in class org.jmol.script.Token
hbondsrasmol - Static variable in class org.jmol.script.Token
hbondssolid - Static variable in class org.jmol.script.Token
HCP - Static variable in class etomica.normalmode.SoftSphereSolidEOS
HCP - Static variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
headType - Variable in class etomica.modules.interfacial.InterfacialSW
HECTO - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺² = 100.
height - Variable in class etomica.graph.view.rasterizer.SVGConverter: Output image height.
height - Variable in class org.jmol.util.GData
Heisenberg - Class in etomica.spin: Simulation of a simple 2D Ising model.
Heisenberg() - Constructor for class etomica.spin.Heisenberg
Heisenberg(Space, int) - Constructor for class etomica.spin.Heisenberg
Helium - Class in etomica.chem.elements: Class for the Helium element.
Helium(String) - Constructor for class etomica.chem.elements.Helium
Helium(String, double) - Constructor for class etomica.chem.elements.Helium
helix - Static variable in class org.jmol.script.Token
helixstep - Static variable in class org.jmol.script.Token
help() - Static method in class etomica.util.numerical.AkimaSplineSmootherMain
helppath - Static variable in class org.jmol.script.Token
heMass - Variable in class etomica.virial.simulations.ModifierTPI
Hermite - Class in org.jmol.util
Hermite() - Constructor for class org.jmol.util.Hermite
hermitelevel - Static variable in class org.jmol.script.Token
HermiteRenderer - Class in org.jmol.g3d: Implementation of hermite curves for drawing smoothed curves that pass through specified points.
HermiteRenderer(Graphics3D) - Constructor for class org.jmol.g3d.HermiteRenderer
HessianDB - Class in etomica.normalmode: MC simulation of FCC soft-sphere model in 3D with tabulation of the collective-coordinate S-matrix.
HessianDB(Space, int, double, double, int, String) - Constructor for class etomica.normalmode.HessianDB
HessianFromFile - Class in etomica.normalmode: MC simulation of FCC soft-sphere model in 3D with tabulation of the collective-coordinate S-matrix.
HessianFromFile() - Constructor for class etomica.normalmode.HessianFromFile
hetero - Static variable in class org.jmol.script.Token
hex - Variable in class etomica.modules.materialfracture.MeterElongation
hex - Variable in class etomica.modules.materialfracture.MeterStrain
hex - Variable in class etomica.modules.materialfracture.StrainColorScheme
Hexahedron - Class in etomica.math.geometry: A polyhedron with six faces, all of which are four-sided polygons.
Hexahedron(ISpace) - Constructor for class etomica.math.geometry.Hexahedron: Constructs a hexahedron to reside in the given space, which determines the type of vertices it will have (e.g.
HexaneVolumeFraction - Class in etomica.models.hexane
HexaneVolumeFraction(Space) - Constructor for class etomica.models.hexane.HexaneVolumeFraction
hh0 - Variable in class etomica.potential.P2HydrogenHinde
hh0 - Variable in class etomica.potential.P2HydrogenHindeAtomic
hh0 - Variable in class etomica.potential.P2HydrogenHindePatkowski
hh0 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
hh0 - Variable in class etomica.potential.P2HydrogenPatkowski
hh0 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
hh1 - Variable in class etomica.potential.P2HydrogenHinde
hh1 - Variable in class etomica.potential.P2HydrogenHindeAtomic
hh1 - Variable in class etomica.potential.P2HydrogenHindePatkowski
hh1 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
hh1 - Variable in class etomica.potential.P2HydrogenPatkowski
hh1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
hidenameinpopup - Static variable in class org.jmol.script.Token
hidenavigationpoint - Static variable in class org.jmol.script.Token
hidenotselected - Static variable in class org.jmol.script.Token
highlight - Static variable in class org.jmol.script.Token
highlightColor - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
highresolution - Static variable in class org.jmol.script.Token
hist - Variable in class etomica.mappedvirial.MeterMeanForce
hist - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
hist - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
hist2 - Variable in class etomica.mappedvirial.MeterMeanForce
histogram - Variable in class etomica.data.AccumulatorHistogram
histogram - Variable in class etomica.data.DataHistogram
histogram - Variable in class etomica.data.HistogramDataSource
histogram - Variable in class etomica.metastable.MeterDensityDistribution
histogram - Variable in class etomica.normalmode.MeterBoltzmannHTTP
histogram - Variable in class etomica.normalmode.MeterTiltHistogram
histogram - Variable in class etomica.normalmode.MeterTiltRotationHistogram
Histogram - Interface in etomica.util: Interface for a class that can tabulate a one-dimensional histogram of data values.
histogram - Variable in class etomica.util.HistogramDiscrete
histogram - Variable in class etomica.util.HistogramNotSoSimple
histogram - Variable in class etomica.util.HistogramReweightedData
histogram - Variable in class etomica.util.HistogramSimple
HistogramCollapsing - Class in etomica.util: Simple Histogram implementation with a static number of bins, but dynamic x range.
HistogramCollapsing() - Constructor for class etomica.util.HistogramCollapsing: Default constructor, making a 100-bin histogram.
HistogramCollapsing(int) - Constructor for class etomica.util.HistogramCollapsing: Makes a new histogram instance having a number of bins given by the argument.
HistogramDataSource - Class in etomica.data: DataSource that simply exposes a Histogram as a DataFunction.
HistogramDataSource(Histogram) - Constructor for class etomica.data.HistogramDataSource
HistogramDiscrete - Class in etomica.util: Histogram class capable of keeping track of how many times each discrete value was passed in, similar to what one would expect from a histogram with very small bin width.
HistogramDiscrete(double) - Constructor for class etomica.util.HistogramDiscrete
HistogramExpanding - Class in etomica.util: Histogram implementation with dynamic x range and number of bins.
HistogramExpanding() - Constructor for class etomica.util.HistogramExpanding: Default constructor, making a histogram with deltaX = 1.0.
HistogramExpanding(double) - Constructor for class etomica.util.HistogramExpanding: Constructs a new instance with the give deltaX bin width and no range.
HistogramExpanding(double, DoubleRange) - Constructor for class etomica.util.HistogramExpanding: Constructs a new instance with the given deltaX bin width and range of X values.
HistogramExpanding(int, DoubleRange) - Constructor for class etomica.util.HistogramExpanding: Makes a new histogram instance, with n bins covering the given range of X values.
HistogramNotSoSimple - Class in etomica.util: Histogram implementation with a static x range and number of bins.
HistogramNotSoSimple(DoubleRange) - Constructor for class etomica.util.HistogramNotSoSimple: Makes a new histogram instance, with the range of x values given by xRange.
HistogramNotSoSimple(int, DoubleRange) - Constructor for class etomica.util.HistogramNotSoSimple: Makes a new histogram instance, with the range of x values given by xRange and n bins.
HistogramReweightedData - Class in etomica.util: Histogram implementation with a static x range and number of bins for reweighted data.
HistogramReweightedData(DoubleRange) - Constructor for class etomica.util.HistogramReweightedData: Makes a new histogram instance, with the range of x values given by xRange.
HistogramReweightedData(int, DoubleRange) - Constructor for class etomica.util.HistogramReweightedData: Makes a new histogram instance, with the range of x values given by xRange and n bins.
HistogramSimple - Class in etomica.util: Simple Histogram implementation with a static x range and number of bins.
HistogramSimple(DoubleRange) - Constructor for class etomica.util.HistogramSimple: Makes a new histogram instance, with the range of x values given by xRange.
HistogramSimple(int, DoubleRange) - Constructor for class etomica.util.HistogramSimple: Makes a new histogram instance, with the range of x values given by xRange and n bins.
histogramUAWf - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
histogramUAWf - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
histogramUAWr - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
histogramUAWr - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
histogramUBWf - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
histogramUBWf - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
histogramUBWr - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
histogramUBWr - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
history - Variable in class etomica.data.AccumulatorHistory
history - Variable in class etomica.data.DataPumpListenerSmart
History - Interface in etomica.util: Interface for an object that keeps track of x and y values and return their history when asked.
history - Variable in class etomica.util.HistoryCollapsing
HistoryCollapsing - Class in etomica.util: History that records a number of values.
HistoryCollapsing() - Constructor for class etomica.util.HistoryCollapsing
HistoryCollapsing(int) - Constructor for class etomica.util.HistoryCollapsing
HistoryCollapsing(int, int) - Constructor for class etomica.util.HistoryCollapsing
HistoryCollapsingAverage - Class in etomica.util: History that records a number of values.
HistoryCollapsingAverage() - Constructor for class etomica.util.HistoryCollapsingAverage
HistoryCollapsingAverage(int) - Constructor for class etomica.util.HistoryCollapsingAverage
HistoryCollapsingDiscard - Class in etomica.util: History that records a number of values.
HistoryCollapsingDiscard() - Constructor for class etomica.util.HistoryCollapsingDiscard
HistoryCollapsingDiscard(int) - Constructor for class etomica.util.HistoryCollapsingDiscard
HistoryCollapsingDiscard(int, int) - Constructor for class etomica.util.HistoryCollapsingDiscard
HistoryComplete - Class in etomica.util: History that records a data from a simulation.
HistoryComplete() - Constructor for class etomica.util.HistoryComplete
HistoryComplete(int) - Constructor for class etomica.util.HistoryComplete
historyED2 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
historyED2 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
historyED2D - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
historyED2D - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
historyED3 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
historyED3 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
historyED3D - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
historyED3D - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
historyEy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
historyEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
historyLength - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
historylevel - Static variable in class org.jmol.script.Token
HistoryScrolling - Class in etomica.util: History that records a number of values, with new ones replacing the earliest ones when the record is full.
HistoryScrolling() - Constructor for class etomica.util.HistoryScrolling
HistoryScrolling(int) - Constructor for class etomica.util.HistoryScrolling
historyTrueEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
HNC - Static variable in class etomica.virial.cluster.ClusterOperations
HNCGenerate(int, char) - Static method in class etomica.virial.HNCGenerator
HNCGenerator - Class in etomica.virial
HNCGenerator() - Constructor for class etomica.virial.HNCGenerator
hNew - Variable in class etomica.integrator.mcmove.MCMoveVolume
hOld - Variable in class etomica.integrator.mcmove.MCMoveVolume
hOptimizer - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
HORIZONTAL - Static variable in class etomica.util.Constants.Alignment
HOTPINK - Static variable in class org.jmol.util.Colix
hover - Static variable in class org.jmol.script.Token
hoverdelay - Static variable in class org.jmol.script.Token
hoverlabel - Static variable in class org.jmol.script.Token
hpType - Variable in class etomica.paracetamol.SpeciesParacetamol
hsb() - Method in interface etomica.graph.model.Bitmap
hsb() - Method in class etomica.graph.model.impl.AbstractBitmap
HSDiameter - Variable in class etomica.dielectric.DHS_NVT.Param
HSDimerNPT - Class in etomica.normalmode: NPT simulation for hard sphere solid using an MCMove that does coordinate scaling with volume changes.
HSDimerNPT(Space, int, boolean, double, double, int[], int, double, double, double) - Constructor for class etomica.normalmode.HSDimerNPT
HSDimerNPT.HSMD3DParameters - Class in etomica.normalmode
HsMc2d - Class in etomica.simulation.prototypes: Simple hard-sphere Monte Carlo simulation in 2D.
HsMc2d() - Constructor for class etomica.simulation.prototypes.HsMc2d
HSMD2D - Class in etomica.simulation.prototypes: Simple hard-sphere molecular dynamics simulation in 2D.
HSMD2D() - Constructor for class etomica.simulation.prototypes.HSMD2D
HSMD2D_noNbr - Class in etomica.simulation.prototypes: Simple hard-sphere molecular dynamics simulation in 2D.
HSMD2D_noNbr(Space) - Constructor for class etomica.simulation.prototypes.HSMD2D_noNbr
HSMD3D - Class in etomica.simulation.prototypes: Three-dimensional hard-sphere molecular dynamics simulation, using neighbor listing.
HSMD3D(ISpace) - Constructor for class etomica.simulation.prototypes.HSMD3D: Sole public constructor, makes a simulation using a 3D space.
HSMD3D(ISpace, HSMD3D.HSMD3DParam) - Constructor for class etomica.simulation.prototypes.HSMD3D
HSMD3D.HSMD3DParam - Class in etomica.simulation.prototypes: Inner class for parameters understood by the HSMD3D constructor
HSMD3DNoNbr - Class in etomica.simulation.prototypes
HSMD3DNoNbr() - Constructor for class etomica.simulation.prototypes.HSMD3DNoNbr
HSMD3DParam() - Constructor for class etomica.simulation.prototypes.HSMD3D.HSMD3DParam
HSMD3DParameters() - Constructor for class etomica.normalmode.HSDimerNPT.HSMD3DParameters
HSMD3DParameters() - Constructor for class etomica.normalmode.HSNPT.HSMD3DParameters
HSMDVParams() - Constructor for class etomica.normalmode.SimHSMDVacancy.HSMDVParams
HSNPT - Class in etomica.normalmode: NPT simulation for hard sphere solid using an MCMove that does coordinate scaling with volume changes.
HSNPT(Space, int, double, boolean, boolean, double) - Constructor for class etomica.normalmode.HSNPT
HSNPT.ActionSummer - Class in etomica.normalmode
HSNPT.ColorSchemeDisplacement - Class in etomica.normalmode
HSNPT.HSMD3DParameters - Class in etomica.normalmode
HSNPT.MyAgent - Class in etomica.normalmode
HSNPT2DGraphic - Class in etomica.normalmode.nptdemo: Simple hard-sphere molecular dynamics simulation in 2D.
HSNPT2DGraphic(HSNPT2DSim) - Constructor for class etomica.normalmode.nptdemo.HSNPT2DGraphic
HSNPT2DGraphic.Applet - Class in etomica.normalmode.nptdemo
HSNPT2DSim - Class in etomica.normalmode.nptdemo: Simple hard-sphere molecular dynamics simulation in 2D.
HSNPT2DSim() - Constructor for class etomica.normalmode.nptdemo.HSNPT2DSim
htElementMap - Static variable in class org.jmol.util.Elements
HTTPSoftSphereApplet - Class in etomica.normalmode: Applet to illustrate HTTP method
HTTPSoftSphereApplet(HTTPSoftSphereSim, double) - Constructor for class etomica.normalmode.HTTPSoftSphereApplet
HTTPSoftSphereApplet.Applet - Class in etomica.normalmode
HTTPSoftSphereApplet.SimOverlapTPSSParams - Class in etomica.normalmode
HTTPSoftSphereSim - Class in etomica.normalmode: Applet to illustrate HTTP method
HTTPSoftSphereSim(Space, int, double) - Constructor for class etomica.normalmode.HTTPSoftSphereSim
hType - Variable in class etomica.AlkaneEH.SpeciesMethane
hType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
hType - Variable in class etomica.models.rowley.SpeciesEthanol
hType - Variable in class etomica.models.rowley.SpeciesMethanol
hType - Variable in class etomica.models.traPPE.SpeciesMethanol
hType - Variable in class etomica.models.water.SpeciesWater3P
hType - Variable in class etomica.models.water.SpeciesWater3POriented
hType - Variable in class etomica.models.water.SpeciesWater4P
hType - Variable in class etomica.models.water.SpeciesWater4PCOM
hType - Variable in class etomica.models.water.SpeciesWater4POriented
hType - Variable in class etomica.virial.SpeciesMethane
hub() - Method in interface etomica.graph.model.Bitmap
hub() - Method in class etomica.graph.model.impl.AbstractBitmap
HYBRID_MC - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
hybridInterval - Variable in class etomica.interfacial.LJMD.LJMDParams
hybridInterval - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
hybridInterval - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
hybridInterval - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
Hydrogen - Class in etomica.chem.elements: Class for the Hydrogen element.
Hydrogen(String) - Constructor for class etomica.chem.elements.Hydrogen
Hydrogen(String, double) - Constructor for class etomica.chem.elements.Hydrogen
hydrogen - Static variable in class org.jmol.script.Token
HydrogenP - Class in etomica.paracetamol: Class for the Hydrogen element.
HydrogenP(String) - Constructor for class etomica.paracetamol.HydrogenP
HydrogenP(String, double) - Constructor for class etomica.paracetamol.HydrogenP
hydrophobic - Static variable in class org.jmol.script.Token
HypernettedChain - Class in etomica.virial: Calculates the hypernetted-chain (HNC) virial coefficients of second to Mth order for any spherically-symmetric Mayer function, fr.
HypernettedChain() - Constructor for class etomica.virial.HypernettedChain
hyperPlanes - Variable in class etomica.math.geometry.Polytope
Hypersphere - Class in etomica.math.geometry: An arbitrary-dimension sphere.
Hypersphere(int) - Constructor for class etomica.math.geometry.Hypersphere: Creates hypersphere of the given dimension, positioned at the origin.
Hypersphere(int, double) - Constructor for class etomica.math.geometry.Hypersphere: Creates hypersphere of the given dimension and radius, positioned at the origin.
hyperVirial - Variable in class etomica.data.meter.MeterHyperVirial
hyperVirial(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
hyperVirial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
hyperVirial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSites
hyperVirial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeOneSite
hyperVirial(IAtomList) - Method in class etomica.potential.P2Ideal: Returns zero.
hyperVirial(IAtomList) - Method in class etomica.potential.P2LJQ
hyperVirial(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
hyperVirial(IAtomList) - Method in class etomica.potential.P2SoftTruncated
hyperVirial(IAtomList) - Method in interface etomica.potential.Potential2Soft: Hypervirial of the pair as given by the du(double) and d2u(double) methods
hyperVirial(IAtomList) - Method in class etomica.potential.Potential2SoftSpherical: Hypervirial of the pair as given by the du(double) and d2u(double) methods
hypot(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The hypotenuse.
hypot(int, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The hypotenuse.
hyType - Variable in class etomica.paracetamol.SpeciesParacetamol

I

I - Variable in class etomica.atom.AtomTypeOrientedSphere
i(double, int) - Method in class etomica.modules.droplet.IntegratorDroplet
I - Variable in class etomica.potential.P3Induction
I - Variable in class etomica.potential.PotentialCalculationPressureTensor
i2roots() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Generate the factors which are 2nd degree polynomials.
iA - Variable in class org.jmol.util.MeshSurface
IAction - Interface in etomica.action
IAPIPotential - Interface in etomica.normalmode: Preliminary interface for proposed IPotential interface
iasdone - Static variable in class etomica.potential.P2WaterPotentialsJankowski
IAssociationHelper - Interface in etomica.association: Interface for a class that is capable of populating a list of atoms in an smer as well as checking the validity of the bonding
IAssociationHelperMolecule - Interface in etomica.association: Interface for a class that is capable of populating a list of molecules in an smer as well as checking the validity of the bonding
IAtom - Interface in etomica.api
IAtomKinetic - Interface in etomica.api: Interface for an atom that holds vectors for velocity.
IAtomList - Interface in etomica.api: Interface for a set of IAtoms.
IAtomOriented - Interface in etomica.atom: Interface for a IAtom that includes an IVector that defines the atom's orientation.
IAtomOrientedKinetic - Interface in etomica.atom: Interface for an Atom that has a position, orientation, velocity and angular velocity.
IAtomPositionDefinition - Interface in etomica.atom: Returns a vector given an atom, thereby defining the position of the atom or atom group.
IAtomType - Interface in etomica.api
IAtomTypeOriented - Interface in etomica.atom
iB - Variable in class org.jmol.util.MeshSurface
IBigValue - Interface in etomica.veos
IBoundary - Interface in etomica.api: Interface for boundary objects that describe the size and periodic nature of the box boundaries.
IBoundaryEvent - Interface in etomica.api
IBoundaryEventManager - Interface in etomica.api
IBoundaryListener - Interface in etomica.api
IBox - Interface in etomica.api
IBoxAtomEvent - Interface in etomica.api
IBoxAtomIndexEvent - Interface in etomica.api
IBoxEvent - Interface in etomica.api
IBoxEventManager - Interface in etomica.api
IBoxIndexEvent - Interface in etomica.api
IBoxListener - Interface in etomica.api
IBoxMoleculeCountEvent - Interface in etomica.api
IBoxMoleculeEvent - Interface in etomica.api
IBoxMoleculeIndexEvent - Interface in etomica.api
iC - Variable in class org.jmol.util.MeshSurface
icc - Variable in class etomica.potential.P2WaterPotentialsJankowski
ICollectionPotential - Interface in etomica.virial.GUI.components
IConformation - Interface in etomica.config
IConformationOriented - Interface in etomica.config
IController - Interface in etomica.action.activity
iCorner - Variable in class etomica.util.Grabber.ActionCornerSetter
iCorner - Variable in class etomica.util.Grabber.CornerSetListener
id - Variable in class etomica.freeenergy.npath.DataSourceEnergies
id - Variable in class etomica.interfacial.MeterWallForce
id - Variable in class etomica.normalmode.MeterDADB
id - Variable in class etomica.normalmode.MeterSolidProps
id - Variable in class etomica.normalmode.MeterSolidPropsLJ
id - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
id - Variable in class etomica.threaded.atom.PotentialMasterListWorker
id - Variable in class etomica.threaded.domain.PotentialMasterListWorker
ID - Variable in class etomica.virial.CoordinatePairLeafSet
ID - Variable in class etomica.virial.CoordinatePairMoleculeSet
id - Variable in enum org.jmol.constant.EnumPalette
IData - Interface in etomica.data: Abstract container of simulation data and information describing it.
IDataInfo - Interface in etomica.data
IDataSink - Interface in etomica.data: A recipient of Data.
IDataSource - Interface in etomica.data
IDEAL_GAS - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
IdenticalFree - Class in etomica.graph.operations: Operation that removes identical graphs
IdenticalFree() - Constructor for class etomica.graph.operations.IdenticalFree
IdenticalGraphFilter - Class in etomica.graph.iterators.filters: Filter that combines graphs that are identical
IdenticalGraphFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.IdenticalGraphFilter
identifier - Static variable in class org.jmol.script.Token
identify - Static variable in class org.jmol.script.Token
identity(int) - Static method in class etomica.math.linearalgebra.Matrix
identity - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
identity - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
identity - Variable in class etomica.models.nitrogen.P2Nitrogen
identity - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
identity - Variable in class etomica.modules.droplet.IntegratorDroplet
identity - Variable in class etomica.potential.EwaldSummation
identity - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
Identity() - Constructor for class etomica.util.Function.Identity
idFontFace - Variable in class org.jmol.util.JmolFont
idFontStyle - Variable in class org.jmol.util.JmolFont
idFreeEnergy(double) - Method in class etomica.statmech.HardSphere: Returns the ideal gas free energy for the given density.
idFreeEnergy(double) - Static method in class etomica.statmech.HardSphereSolid: Returns the ideal gas free energy for the given density.
iDiagram - Variable in class etomica.virial.ClusterSumStickyEF
iDipole - Variable in class etomica.potential.P2ReactionFieldDipole
iDipole - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
idonl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
ids - Variable in class etomica.virial.PotentialEmulCached
idx - Variable in class etomica.lattice.crystal.Primitive
IEGenerator - Class in etomica.virial
IEGenerator() - Constructor for class etomica.virial.IEGenerator
IElement - Interface in etomica.api
iEmbed - Variable in class etomica.potential.P2WaterPotentialsJankowski
IEtomicaDataInfo - Interface in etomica.data
IEtomicaDataInfoFactory - Interface in etomica.data
IEtomicaDataSource - Interface in etomica.data: Interface for an object that can provide Data objects on request.
IEvent - Interface in etomica.util
IEventManager - Interface in etomica.util
ifactor() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Factorization into integer polynomials.
Ifactor - Class in etomica.veos.bigdecimal: Factored integers.
Ifactor(int) - Constructor for class etomica.veos.bigdecimal.Ifactor: Constructor given an integer.
Ifactor(BigInteger) - Constructor for class etomica.veos.bigdecimal.Ifactor: Constructor given a BigInteger .
Ifactor(Vector<Integer>) - Constructor for class etomica.veos.bigdecimal.Ifactor: Constructor given a list of exponents of the prime factor decomposition.
Ifactor(Ifactor) - Constructor for class etomica.veos.bigdecimal.Ifactor: Copy constructor.
IFLGST - Variable in class etomica.math.Gamma
IFunction - Interface in etomica.api
ig - Variable in class etomica.modules.mu.MeterDensitySides
ignoredAtomType - Variable in class etomica.modules.chainequilibrium.MeterChainLength
ignoreOverlap - Variable in class etomica.action.SimulationRestart
ignoreOverlap - Variable in class etomica.modules.mu.P2SquareWellOneSide
ignoreOverlap - Variable in class etomica.potential.P2HardSphere
ignoreOverlap - Variable in class etomica.potential.P2PenetrableSquareWell
ignoreOverlap - Variable in class etomica.potential.P2SquareWell
ignoreOverlap - Variable in class etomica.potential.P2SquareWellRobust
iGraph - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
IIntegrator - Interface in etomica.api
IIntegratorEvent - Interface in etomica.api
IIntegratorEventManager - Interface in etomica.api
IIntegratorListener - Interface in etomica.api
IIntegratorListenerMD - Interface in etomica.api
ijInit(double[], double[][], Unit) - Method in class etomica.models.co2.P2CO2Hellmann
ijk - Variable in class etomica.models.water.P2WaterSzalewicz
ijRTensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
ijRTensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
ijRTensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
ijRTensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
ijTensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
ijTensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
ijTensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
ijTensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
IListener - Interface in etomica.util
imageOrigins(int) - Method in class etomica.space.Boundary: Set of vectors describing the displacements needed to translate the central image to all of the periodic images.
imageOrigins(int) - Method in class etomica.space.BoundaryDeformablePeriodic
imageOrigins(int) - Method in class etomica.space.BoundaryRectangular: Returns a set of image origins for a set of periodic image shells.
imageOrigins(int) - Method in class etomica.space.BoundaryRectangularNonperiodic: Returns a zero-length vector.
imageOrigins(int) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
imageOut(String) - Method in class etomica.graph.viewer.GraphMap
ImagePanel() - Constructor for class etomica.util.Grabber.ImagePanel: Constructor sets default size of the plot
ImagePanel(Color, int, int) - Constructor for class etomica.util.Grabber.ImagePanel
ImageShell - Class in g3dsys.images
ImageShell(G3DSys) - Constructor for class g3dsys.images.ImageShell
imagestate - Static variable in class org.jmol.script.Token
imaginaryT - Variable in class etomica.normalmode.MeterHarmonicCoordinate
imaginaryT - Variable in class etomica.normalmode.MeterHarmonicEnergy
imaginaryT - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
imaginaryT - Variable in class etomica.normalmode.MeterNormalMode
imaginaryYm(int, int, double, double) - Static method in class etomica.math.SphericalHarmonics
imagine() - Method in class etomica.math.Complex: Imaginary part of this Complex number,the y-coordinate in rectangular coordinates.
imax - Variable in class etomica.conjugategradient.ConjugateGradients
imax - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
imax - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
imax - Variable in class etomica.conjugategradient.SteepestDescent
imgPanel - Variable in class etomica.util.Grabber
IMolecularModel_SpeciesFactory - Interface in etomica.virial.GUI.models
IMolecule - Interface in etomica.api: Interface for an IMolecule
iMolecule - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
iMolecule - Variable in class etomica.virial.MCMoveClusterRingScale
IMoleculeKinetic - Interface in etomica.atom: Interface for an molecule that holds vectors for velocity.
IMoleculeList - Interface in etomica.api: Interface for a set of IAtoms.
IMoleculeOriented - Interface in etomica.atom: Interface for a IAtom that includes an IVector that defines the atom's position.
IMoleculeOrientedKinetic - Interface in etomica.atom: Interface for an Atom that has a position, orientation, velocity and angular velocity.
IMoleculePositioned - Interface in etomica.atom
iMon - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
iMonomer - Variable in class etomica.potential.P2WaterPotentialsJankowski
inc() - Method in interface etomica.graph.model.Bitmap: Increments the integer value of this bitmap by one: bitmap++.
inc() - Method in class etomica.graph.model.impl.AbstractBitmap
includeAntibiasErr - Variable in class etomica.overlap.DataOverlap
includeLrc - Variable in class etomica.atom.iterator.IteratorDirective: Flag indicating whether long-range correction contributions should be included in calculation.
includeM - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
includeM - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
INCLUSIVE - Static variable in class etomica.data.DataSourceUniform.LimitType: Limit type indicating that limit is included in range, and that it equals the extreme value.
INCOMPATIBLE_TYPES - Static variable in class etomica.compatibility.Feature
increment(int[]) - Method in class etomica.lattice.RectangularLattice
increment(int) - Method in class org.jmol.script.ScriptVariable
ind3_beta - Static variable in class etomica.models.water.P2WaterSzalewicz
ind3_gamma - Static variable in class etomica.models.water.P2WaterSzalewicz
ind3_R0 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_beta - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_C10 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_C6 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_C8 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_charge - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_d1 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_d10 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_d6 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_d8 - Static variable in class etomica.models.water.P2WaterSzalewicz
ind_lin - Variable in class etomica.models.water.P2WaterSzalewicz
inDataInfo - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
index - Variable in class etomica.action.activity.ControllerEvent.Type
index - Variable in class etomica.atom.Atom
index - Variable in class etomica.atom.AtomTypeLeaf
index - Variable in class etomica.atom.iterator.ApiIndexList
index - Variable in class etomica.atom.Molecule
index - Variable in class etomica.box.BoxAtomIndexEvent
index - Variable in class etomica.box.BoxIndexEvent
index - Variable in class etomica.box.BoxMoleculeIndexEvent
index - Variable in class etomica.data.AccumulatorAverage.StatType
index - Variable in class etomica.data.AccumulatorAverageBlockless.StatType
index - Variable in class etomica.data.AccumulatorAverageBlocklessSlim.StatType
index - Variable in class etomica.data.DataSet.DataSetSink
index - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
index - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
index - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
index - Variable in class etomica.species.Species
index - Variable in class org.jmol.script.ScriptVariable
index - Variable in class org.jmol.util.Point3fi
indexaC - Static variable in class etomica.models.rowley.SpeciesEthanol
indexaC - Static variable in class etomica.models.rowley.SpeciesMethanol
indexaH - Static variable in class etomica.models.rowley.SpeciesEthanol
indexaH - Static variable in class etomica.models.rowley.SpeciesMethanol
indexAtom1 - Static variable in class etomica.normalmode.SpeciesHSDimer
indexAtom2 - Static variable in class etomica.normalmode.SpeciesHSDimer
indexC - Static variable in class etomica.AlkaneEH.SpeciesMethane
indexC - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
indexC - Static variable in class etomica.models.rowley.SpeciesEthanol
indexC - Static variable in class etomica.models.water.SpeciesWater4PCOM
indexC - Static variable in class etomica.paracetamol.SpeciesParacetamol
indexC - Static variable in class etomica.virial.SpeciesMethane
indexC - Static variable in class etomica.virial.SpeciesTraPPECO2
indexC1 - Static variable in class etomica.virial.SpeciesAnthracene3site464
indexC1 - Static variable in class etomica.virial.SpeciesAnthracene3site545
indexC1 - Static variable in class etomica.virial.SpeciesPh3site464
indexC1 - Static variable in class etomica.virial.SpeciesPh3site545
indexC1 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexC1 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexC1 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexC2 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexC2 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexC2 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexC3 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexC3 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexC4 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexC4 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexC_3_1 - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
indexC_3_1 - Variable in class etomica.virial.SpeciesAlkaneEH
indexC_3_2 - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
indexC_3_2 - Variable in class etomica.virial.SpeciesAlkaneEH
indexCenter - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
indexCH1 - Static variable in class etomica.virial.SpeciesAnthracene3site464
indexCH1 - Static variable in class etomica.virial.SpeciesAnthracene3site545
indexCH1 - Static variable in class etomica.virial.SpeciesPh3site464
indexCH1 - Static variable in class etomica.virial.SpeciesPh3site545
indexCH1 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH1 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH1 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH10 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH10 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH2 - Static variable in class etomica.virial.SpeciesAnthracene3site464
indexCH2 - Static variable in class etomica.virial.SpeciesAnthracene3site545
indexCH2 - Static variable in class etomica.virial.SpeciesPh3site464
indexCH2 - Static variable in class etomica.virial.SpeciesPh3site545
indexCH2 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH2 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH2 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH3 - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
indexCH3 - Static variable in class etomica.models.traPPE.SpeciesMethanol
indexCH3 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH3 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH3 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH4 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH4 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH4 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH5 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH5 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH5 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH6 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH6 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH6 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH7 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH7 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH7 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH8 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH8 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
indexCH8 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexCH9 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
indexCH9 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
indexDBO - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
indexed - Variable in class etomica.graph.view.rasterizer.SVGConverter: Should output Image be indexed .
indexer - Variable in class etomica.data.DataDistributer
indexF1 - Static variable in class etomica.virial.Species7SiteRigidSF6
indexF2 - Static variable in class etomica.virial.Species7SiteRigidSF6
indexF3 - Static variable in class etomica.virial.Species7SiteRigidSF6
indexF4 - Static variable in class etomica.virial.Species7SiteRigidSF6
indexF5 - Static variable in class etomica.virial.Species7SiteRigidSF6
indexF6 - Static variable in class etomica.virial.Species7SiteRigidSF6
indexH - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
indexH - Static variable in class etomica.models.traPPE.SpeciesMethanol
indexH - Static variable in class etomica.paracetamol.SpeciesParacetamol
indexH1 - Static variable in class etomica.AlkaneEH.SpeciesMethane
indexH1 - Static variable in class etomica.models.rowley.SpeciesMethanol
indexH1 - Static variable in class etomica.models.water.SpeciesWater3P
indexH1 - Static variable in class etomica.models.water.SpeciesWater3POriented
indexH1 - Static variable in class etomica.models.water.SpeciesWater4P
indexH1 - Static variable in class etomica.models.water.SpeciesWater4PCOM
indexH1 - Static variable in class etomica.models.water.SpeciesWater4POriented
indexH1 - Static variable in class etomica.virial.SpeciesMethane
indexH1a - Static variable in class etomica.models.rowley.SpeciesEthanol
indexH1b - Static variable in class etomica.models.rowley.SpeciesEthanol
indexH2 - Static variable in class etomica.AlkaneEH.SpeciesMethane
indexH2 - Static variable in class etomica.models.water.SpeciesWater3P
indexH2 - Static variable in class etomica.models.water.SpeciesWater3POriented
indexH2 - Static variable in class etomica.models.water.SpeciesWater4P
indexH2 - Static variable in class etomica.models.water.SpeciesWater4PCOM
indexH2 - Static variable in class etomica.models.water.SpeciesWater4POriented
indexH2 - Static variable in class etomica.virial.SpeciesMethane
indexH2a - Static variable in class etomica.models.rowley.SpeciesEthanol
indexH2a - Static variable in class etomica.models.rowley.SpeciesMethanol
indexH2b - Static variable in class etomica.models.rowley.SpeciesEthanol
indexH2b - Static variable in class etomica.models.rowley.SpeciesMethanol
indexH2c - Static variable in class etomica.models.rowley.SpeciesEthanol
indexH3 - Static variable in class etomica.AlkaneEH.SpeciesMethane
indexH3 - Static variable in class etomica.virial.SpeciesMethane
indexH4 - Static variable in class etomica.AlkaneEH.SpeciesMethane
indexH4 - Static variable in class etomica.virial.SpeciesMethane
indexHp - Static variable in class etomica.paracetamol.SpeciesParacetamol
indexIterator - Variable in class etomica.config.ConfigurationLattice
indexIterator - Variable in class etomica.config.ConfigurationLatticeSimple
IndexIterator - Interface in etomica.lattice: Loops through the set of indexes appropriate to a lattice of given size.
indexIterator - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
indexIterator - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
IndexIterator - Interface in g3dsys.control
IndexIteratorIncreasing - Class in etomica.lattice: Iterator that returns indices in increasing order, starting at 0 and ending including all indices where |i| <= max, where i are the components of the index.
IndexIteratorIncreasing(int) - Constructor for class etomica.lattice.IndexIteratorIncreasing
IndexIteratorRectangular - Class in etomica.lattice: Iterates arrays of int, such that 0 <= a[0] <= size[0], 0 <= a[1] <= size[1], etc., thereby spanning a rectangular region.
IndexIteratorRectangular(int) - Constructor for class etomica.lattice.IndexIteratorRectangular: Constructs iterator that returns int arrays of length D.
IndexIteratorReflecting - Class in etomica.lattice: Generates iterates by alternately keeping or flipping the sign of each element of iterates generated by another iterator.
IndexIteratorReflecting(IndexIterator) - Constructor for class etomica.lattice.IndexIteratorReflecting: Constructs iterator to generate reflections from iterates of given iterator.
IndexIteratorSizable - Interface in etomica.lattice: Interface for an iterator in which the number of indices in each dimension may be specified.
IndexIteratorTriangular - Class in etomica.lattice: Iterates arrays of int such that a[0] >= a[1] >= ...
IndexIteratorTriangular(int) - Constructor for class etomica.lattice.IndexIteratorTriangular: Constructs iterator that will return int arrays of length D.
IndexIteratorTriangularPermutations - Class in etomica.lattice: Generates all unique iterates formed as permutations of iterates given by IndexIteratorTriangular with allowEqualElements set to true.
IndexIteratorTriangularPermutations(int) - Constructor for class etomica.lattice.IndexIteratorTriangularPermutations
indexM - Static variable in class etomica.models.water.SpeciesWater4P
indexM - Static variable in class etomica.models.water.SpeciesWater4PCOM
indexM - Static variable in class etomica.models.water.SpeciesWater4POriented
indexN - Static variable in class etomica.paracetamol.SpeciesParacetamol
indexN1 - Static variable in class etomica.models.nitrogen.SpeciesN2
indexN1 - Static variable in class etomica.models.nitrogen.SpeciesN2B
indexN1 - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
indexN2 - Static variable in class etomica.models.nitrogen.SpeciesN2
indexN2 - Static variable in class etomica.models.nitrogen.SpeciesN2B
indexN2 - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
indexO - Static variable in class etomica.models.rowley.SpeciesEthanol
indexO - Static variable in class etomica.models.rowley.SpeciesMethanol
indexO - Static variable in class etomica.models.traPPE.SpeciesMethanol
indexO - Static variable in class etomica.models.water.SpeciesWater3P
indexO - Static variable in class etomica.models.water.SpeciesWater3POriented
indexO - Static variable in class etomica.models.water.SpeciesWater4P
indexO - Static variable in class etomica.models.water.SpeciesWater4PCOM
indexO - Static variable in class etomica.models.water.SpeciesWater4POriented
indexO - Static variable in class etomica.paracetamol.SpeciesParacetamol
indexOf(IAtom) - Method in class etomica.atom.AtomArrayList
indexOf(IMolecule) - Method in class etomica.atom.MoleculeArrayList
indexOf(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
indexOf(Object) - Method in class etomica.util.ObjectArrayList: Searches for the first occurence of the given argument, testing for equality using the equals method.
indexOf(String) - Method in class org.jmol.util.StringXBuilder
indexOf2(String, int) - Method in class org.jmol.util.StringXBuilder
indexOleft - Static variable in class etomica.virial.SpeciesTraPPECO2
indexOright - Static variable in class etomica.virial.SpeciesTraPPECO2
indexP1left - Static variable in class etomica.models.nitrogen.SpeciesN2
indexP1left - Static variable in class etomica.models.nitrogen.SpeciesN2B
indexP1left - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
indexP1right - Static variable in class etomica.models.nitrogen.SpeciesN2
indexP1right - Static variable in class etomica.models.nitrogen.SpeciesN2B
indexP1right - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
indexP2left - Static variable in class etomica.models.nitrogen.SpeciesN2
indexP2left - Static variable in class etomica.models.nitrogen.SpeciesN2B
indexP2right - Static variable in class etomica.models.nitrogen.SpeciesN2
indexP2right - Static variable in class etomica.models.nitrogen.SpeciesN2B
indexReservoir - Variable in class etomica.box.Box
indexS - Static variable in class etomica.virial.Species7SiteRigidSF6
indexSBO - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
indexSelectedSpecies - Variable in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
indexX - Static variable in class etomica.models.rowley.SpeciesEthanol
indexX - Static variable in class etomica.models.rowley.SpeciesMethanol
indices - Variable in class etomica.virial.cluster.PermutationIterator
indN_iter() - Method in class etomica.models.water.P2WaterSzalewicz: Compute the iterative induction between N water molecules using several polarization centers in the molecular plane
INeighborListListener - Interface in etomica.nbr.list
INeighborListListenerMolecular - Interface in etomica.nbr.list.molecule
inflate - Variable in class etomica.integrator.IntegratorGear4NPH
inflate - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
inflate - Variable in class etomica.integrator.mcmove.MCMoveVolume
inflate - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
inflate - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
inflate - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
inflate - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
inflate - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
inflate - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
inflate - Variable in class etomica.normalmode.MCMoveVolumeSolid
inflate - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
inflate(IBoundary) - Method in class etomica.space.BoundaryEventManager
inflateEvent - Variable in class etomica.space.Boundary
info - Static variable in class org.jmol.script.Token
info(String) - Method in class org.jmol.util.DefaultLogger
info(String) - Static method in class org.jmol.util.Logger: og* Writes a log at INFO level.
info(String) - Method in interface org.jmol.util.LoggerInterface: Writes a log at INFO level.
info2 - Variable in class etomica.meam.EFSTungsten
info2 - Variable in class etomica.meam.MEAM_3DMDwithGB
info2 - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
info2 - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
info2 - Variable in class etomica.meam.MEAM_MC
info2 - Variable in class etomica.meam.MEAMMd3D
info2 - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
inGreyscaleMode - Variable in class org.jmol.util.GData
INHERIT_ALL - Static variable in class org.jmol.util.Colix
INHERIT_COLOR - Static variable in class org.jmol.util.Colix
init(ISimulation) - Method in class etomica.atom.AtomTypeAgentManager: Sets the SpeciesRoot for which this AtomAgentManager will manage AtomType agents.
init(ISimulation) - Method in class etomica.atom.SpeciesAgentManager: Sets the SpeciesRoot for which this AtomAgentManager will manage AtomType agents.
init() - Method in class etomica.graph.viewer.GraphMap
init() - Method in class etomica.graphics.DeviceNSelector
init() - Method in class etomica.graphics.DisplayPolytope.Applet
init() - Method in class etomica.modules.adsorption.AdsorptionGraphic.Applet
init() - Method in class etomica.modules.catalysis.CatalysisGraphic.Applet
init() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet
init() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet
init() - Method in class etomica.modules.clustergenerator.MyApplet
init() - Method in class etomica.modules.colloid.ColloidGraphic.Applet
init() - Method in class etomica.modules.crystalviewer.CrystalViewer.Applet
init() - Method in class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet
init() - Method in class etomica.modules.droplet.DropletAtomicGraphic.Applet
init() - Method in class etomica.modules.droplet.DropletGraphic.Applet
init() - Method in class etomica.modules.ensembles.LJMCGraphic.Applet
init() - Method in class etomica.modules.entropylottery.EntropyLotteryGraphic.Applet
init() - Method in class etomica.modules.insertion.InsertionGraphic.Applet
init() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.Applet
init() - Method in class etomica.modules.joulethomson.JouleThomson.Applet
init() - Method in class etomica.modules.ljmd.LjmdGraphic.Applet
init() - Method in class etomica.modules.materialfracture.MaterialFractureGraphic.Applet
init() - Method in class etomica.modules.mu.MuGraphic.Applet
init() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet
init() - Method in class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet
init() - Method in class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet
init() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet
init() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet
init() - Method in class etomica.modules.osmosis.Osmosis.Applet
init() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet
init() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic: Initialize all the bits based on previously set doConfigButton and doRDF.
init() - Method in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet
init() - Method in class etomica.modules.rheology.RheologyGraphic.Applet
init() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet
init() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet
init() - Method in class etomica.modules.sam.SamGraphic.Applet
init() - Method in class etomica.modules.swmd.SwmdGraphic.Applet
init() - Method in class etomica.modules.vle.B2Fit.Applet
init() - Method in class etomica.modules.vle.VLE.Applet
init() - Method in class etomica.normalmode.DeviceCellNumXYSlider
init() - Method in class etomica.normalmode.HTTPSoftSphereApplet.Applet
init() - Method in class etomica.normalmode.MCMovePhaseAngle
init() - Method in class etomica.normalmode.MCMoveWV
init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay1D.Applet
init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet
init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet
init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D.Applet
init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet
init() - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic.Applet
init() - Method in class etomica.normalmode.SimLJVacancy.Applet
init() - Method in class etomica.rotation.DipoleBox.Applet
init() - Method in class etomica.rotation.DipoleBoxMatrix.Applet
init() - Method in class etomica.rotation.SingleDipole.Applet
init() - Method in class etomica.rotation.SingleDumbellRattle.Applet
init() - Method in class etomica.rotation.SingleDumbellShake.Applet
init() - Method in class etomica.rotation.SingleWater.Applet
init() - Method in class etomica.rotation.SingleWaterMatrix.Applet
init() - Method in class etomica.rotation.SingleWaterRattle.Applet
init() - Method in class etomica.rotation.SingleWaterShake.Applet
init() - Method in class etomica.rotation.WaterBox.Applet
init() - Method in class etomica.rotation.WaterDroplet.Applet
init() - Method in class etomica.rotation.WaterDropletMatrix.Applet
init() - Method in class etomica.rotation.WaterDropletRattle.Applet
init() - Method in class etomica.rotation.WaterDropletShake.Applet
init() - Method in class etomica.rotation.WaterTrimer.Applet
init() - Method in class etomica.rotation.WaterTrimerRattle.Applet
init() - Method in class etomica.rotation.WaterTrimerShake.Applet
init() - Method in class etomica.simulation.prototypes.LjMd3D.Applet
init() - Method in class etomica.species.SpeciesOriented
init() - Method in class etomica.thermointegration.LjMc3D.Applet
init() - Method in class etomica.util.numerical.AkimaSplineSmootherApp.Applet
init(int) - Method in class etomica.util.numerical.AkimaSplineSmootherApp
init() - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.Applet
init(int) - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp
init() - Method in class etomica.veos.bigdecimal.Wigner3jGUI
init() - Method in class etomica.virial.cluster.VirialDiagrams
init() - Method in class etomica.virial.cluster.VirialDiagramsPT
init() - Method in class etomica.virial.simulations.SimulationVirial
init() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
init() - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
init() - Method in class etomica.virial.SpeciesFactorySpheres2
initAlpha() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
initAlpha() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
initAlpha() - Method in class etomica.normalmode.MeterOverlapSwitch
initAlpha() - Method in class etomica.normalmode.MeterTargetTP
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
initBlockAccumulator() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
initBox(IBox) - Method in class etomica.normalmode.P1ConstraintNbr: Assigns & keeps track of a set of neighbors for each box
initC - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
initCar - Variable in class etomica.modules.render.RenderMD.RenderMDParam
initCellEditor(TableModel) - Method in class etomica.graphics.DeviceTable
initComponents() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
initComponents() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
initialize() - Method in class etomica.association.AssociationManager
initialize() - Method in class etomica.association.AssociationManagerMolecule
initialize() - Method in class etomica.graphics.DisplayPolytopeCanvas2D
initialize(long) - Method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
initialize(long) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
initialize(long) - Method in class etomica.models.nitrogen.SimOverlapBetaN2TP
initialize(long) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
initialize(long) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
initialize(long) - Method in class etomica.normalmode.SimEinStep2
initialize(long) - Method in class etomica.normalmode.SimEinStep2HCP
initialize(long) - Method in class etomica.normalmode.SimLJHTTISuper
initialize(long) - Method in class etomica.normalmode.SimLJHTTISuperHCP
initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereDP
initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereEin
initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereTP
initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereTPHCP
initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
initialize() - Method in class etomica.potential.P2QChemInterpolated
initialize(ApiPlatform) - Method in class org.jmol.g3d.Graphics3D
initialize(ApiPlatform) - Method in class org.jmol.util.GData
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2TP
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
initializeConfigFromFile(String) - Method in class etomica.normalmode.SimFluidSoftSphere
initializeConfiguration(String) - Method in class etomica.dimer.SimDimerLJadatom
initializeConfiguration(String) - Method in class etomica.dimer.SimDimerMEAMadatom
initializeConfiguration(String) - Method in class etomica.dimer.SimDimerMEAMGB
initializeConfiguration(String) - Method in class etomica.kmc.SimKMCLJadatom
initializeConfiguration(String) - Method in class etomica.kmc.SimKMCMEAMadatom
initializeConformation(IMolecule) - Method in interface etomica.api.ISpecies: Initializes the molecule's IAtoms in their standard arrangement.
initializeConformation(IMolecule, IVector) - Method in class etomica.models.nitrogen.SpeciesN2
initializeConformation(IMolecule) - Method in class etomica.species.Species
initializeCoordinates() - Method in class etomica.action.IntegratorDimerApproach
initializeCoordinates(IBox) - Method in interface etomica.config.Configuration: Defines the placement of the molecules.
initializeCoordinates(IBox) - Method in class etomica.config.ConfigurationFile
initializeCoordinates(IBox) - Method in class etomica.config.ConfigurationFileBinary
initializeCoordinates(IBox) - Method in class etomica.config.ConfigurationLattice: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox, ISpecies) - Method in class etomica.config.ConfigurationLattice
initializeCoordinates(IBox) - Method in class etomica.config.ConfigurationLatticeSimple: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox) - Method in class etomica.config.ConfigurationLatticeWithPlane: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox) - Method in class etomica.config.ConfigurationZincblende: Initializes positions of atoms to the zincblende structure.
initializeCoordinates(IBox) - Method in class etomica.config.GrainBoundaryConfiguration: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox) - Method in class etomica.config.GrainBoundaryTiltConfiguration
initializeCoordinates(IBox) - Method in class etomica.interfacial.ConfigurationLammps
initializeCoordinates(int[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
initializeCoordinates(int[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
initializeCoordinates(IBox) - Method in class etomica.models.water.ConfigurationFileTIP4P
initializeCoordinates(IBox) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
initializeCoordinates(IBox) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
initializeCoordinates(IBox) - Method in class etomica.modules.colloid.ConfigurationColloid
initializeCoordinates(IBox) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
initializeCoordinates(IBox) - Method in class etomica.modules.droplet.ConfigurationDroplet
initializeCoordinates(IBox) - Method in class etomica.modules.entropylottery.ConfigurationZero
initializeCoordinates(IBox) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
initializeCoordinates(IBox) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
initializeCoordinates(IBox) - Method in class etomica.modules.sam.ConfigurationSAM
initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinition
initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
initializeCoordinates(IBox) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(IBox) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice: Places the molecules in the given box on the positions of the lattice.
initializeCoordinates(int[]) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
initializeCoordinates(IBox) - Method in class etomica.rotation.ConfigurationWater108
initializeCoordinates(IBox) - Method in class etomica.rotation.ConfigurationWater108TIP4P
initializeCoordinates(IBox) - Method in class etomica.rotation.ConfigurationWater256
initializeCoordinates(IBox) - Method in class etomica.rotation.ConfigurationWater3
initializeCoordinates(IBox) - Method in class etomica.rotation.ConfigurationWater3_3P
initializeCoordinates(IBox) - Method in class etomica.spin.ConfigurationAligned: Sets all spins to be aligned in the +x direction
initializeCoordinates(IBox) - Method in class etomica.virial.ConfigurationCluster
initializeCoordinates(IBox, boolean, boolean) - Method in class etomica.virial.ConfigurationClusterAceticAcid
initializeCoordinates(IBox) - Method in class etomica.virial.ConfigurationClusterChain
initializeCoordinates(IBox) - Method in class etomica.virial.ConfigurationClusterChainFourSites
initializeCoordinates(IBox) - Method in class etomica.virial.ConfigurationClusterMove
initializeCoordinates(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
initializeCoordinates(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates(IBox) - Method in class etomica.zeolite.ConfigurationFileXYZ
initializeCoordinates2(IBox, boolean, boolean) - Method in class etomica.virial.ConfigurationClusterAceticAcid
initializeCoordinates2(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
initializeCoordinates2(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates3(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
initializeCoordinates3(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates4(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
initializeCoordinates4(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinates4Mol(IBox, char, char, char, char, char, int, int) - Method in class etomica.virial.ConfigurationClusterAceticAcid
initializeCoordinates5(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
initializeCoordinates5(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinatesBranch(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
initializeCoordinatesER(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
initializeCoordinatesER(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinatesRef(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
initializeCoordinatesTetramer(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
initializeCoordinatesTrimer(IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
initialized - Variable in class etomica.integrator.Integrator
initialized() - Method in class etomica.integrator.IntegratorEventManager
initialized - Variable in class etomica.models.water.OrientationCalcWater3P
initialized - Variable in class etomica.models.water.OrientationCalcWater4P
initialized - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
initialized - Variable in class etomica.nbr.list.NeighborListManager
initialized - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
InitializeMolecules(ConfigurationLatticeWithPlane, SimulationRestart) - Constructor for class etomica.modules.osmosis.Osmosis.InitializeMolecules
initializePositions(IAtomList) - Method in class etomica.AlkaneEH.ConformationAlkaneEH
initializePositions(IAtomList) - Method in class etomica.AlkaneEH.ConformationMethane
initializePositions(IAtomList) - Method in class etomica.config.ConformationChain: Places a set of atoms in a linearly connected fashion.
initializePositions(IAtomList) - Method in class etomica.config.ConformationChainLinear
initializePositions(IAtomList) - Method in class etomica.config.ConformationGeneric
initializePositions(IAtomList) - Method in class etomica.config.ConformationLinear
initializePositions(IAtomList) - Method in class etomica.config.ConformationWater
initializePositions(IAtomList) - Method in interface etomica.config.IConformation: Defined by subclass to assign coordinates to the atoms in the given list.
initializePositions(IAtomList, IOrientation) - Method in interface etomica.config.IConformationOriented: Assign coordinates to the atoms in the given list using the given orientation for the molecule.
initializePositions(IAtomList) - Method in class etomica.models.nitrogen.ConformationNitrogen
initializePositions(IAtomList, IVector) - Method in class etomica.models.nitrogen.ConformationNitrogen
initializePositions(IAtomList) - Method in class etomica.models.nitrogen.ConformationNitrogenShellModel
initializePositions(IAtomList) - Method in class etomica.models.OPLS.ConformationAceticAcid
initializePositions(IAtomList) - Method in class etomica.models.rowley.ConformationEthanol
initializePositions(IAtomList) - Method in class etomica.models.rowley.ConformationMethanol
initializePositions(IAtomList) - Method in class etomica.models.traPPE.ConformationMethanol
initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWater3P
initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWaterGCPM
initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWaterGCPMCOM
initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWaterTIP4P
initializePositions(IAtomList) - Method in class etomica.models.water.OrientationCalcWater3P
initializePositions(IAtomList) - Method in class etomica.models.water.OrientationCalcWater4P
initializePositions(IAtomList) - Method in class etomica.modules.dcvgcmd.ConformationTube
initializePositions(IAtomList) - Method in class etomica.modules.rheology.ConformationPolymer
initializePositions(IAtomList, IOrientation) - Method in class etomica.normalmode.ConformationHSDimer
initializePositions(IAtomList) - Method in class etomica.normalmode.ConformationHSDimer
initializePositions(IAtomList) - Method in class etomica.paracetamol.ConformationParacetamol
initializePositions(IAtomList) - Method in class etomica.paracetamol.ConformationParacetamolMonoclinic
initializePositions(IAtomList) - Method in class etomica.paracetamol.ConformationParacetamolOrthorhombic
initializePositions(IAtomList) - Method in class etomica.virial.Conformation7SiteRigidSF6
initializePositions(IAtomList) - Method in class etomica.virial.ConformationAlkaneEH
initializePositions(IAtomList) - Method in class etomica.virial.ConformationAnthracene3site
initializePositions(IAtomList) - Method in class etomica.virial.ConformationAnthraceneTraPPE
initializePositions(IAtomList) - Method in class etomica.virial.ConformationCO2
initializePositions(IAtomList) - Method in class etomica.virial.ConformationMethane
initializePositions(IAtomList) - Method in class etomica.virial.ConformationNaphthaleneTraPPE
initializePositions(IAtomList) - Method in class etomica.virial.ConformationPh3site
initializePositions(IAtomList) - Method in class etomica.virial.ConformationPhenanthreneTraPPE
initializeSim() - Method in class etomica.threads.AtomDecompositionMD
initializing - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
initializing - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
initialLatticeEnergy - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
initialSeed - Variable in class etomica.data.AccumulatorAverageCollapsingLog
initialSolute - Static variable in class etomica.modules.osmosis.OsmosisSim
initialSolvent - Static variable in class etomica.modules.osmosis.OsmosisSim
initialState(Graph, Graph) - Static method in class etomica.graph.isomorphism.Match: Initial search state with the default isomorphism test algorithm.
initialU - Static variable in class etomica.models.clathrates.ClathrateHarmonicFE
initialU - Static variable in class etomica.models.clathrates.MinimizationTIP4P
initialU - Static variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
initLat - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
initMetaDataComparator() - Static method in class etomica.virial.cluster.VirialDiagrams
initMetaDataComparator() - Static method in class etomica.virial.cluster.VirialDiagramsPT
initMolecOrientation - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
initMolecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
initMolecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
initMolecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
initNominalU(IMoleculeList) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
initNominalU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen: Override if nominal U is more than the lattice position of the molecule Number of molecules equals to basis atoms initNomial is the method to define the initial orientation of the molecule
initNominalU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox: Override if nominal U is more than the lattice position of the molecule Number of molecules equals to basis atoms initNomial is the method to define the initial orientation of the molecule
initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinition: Initializes the CoordinateDefinition for the given molecule and associates the molecule with the given index.
initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionLeaf
initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMolecule: Override if nominal U is more than the lattice position of the molecule
initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation: Override if nominal U is more than the lattice position of the molecule
initNominalU(IMoleculeList) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol: Override if nominal U is more than the lattice position of the molecule
initP() - Method in class etomica.normalmode.MeterDDP
initP() - Method in class etomica.normalmode.MeterDP
initPotential(ISpace, SpeciesAceticAcid, PotentialGroup) - Static method in class etomica.models.OPLS.AceticAcidModPotentialHelper
initPotential(ISpace, SpeciesAceticAcid, PotentialGroup) - Static method in class etomica.models.OPLS.AceticAcidPotentialHelper
initPotential(ISpace, SpeciesEthanol, PotentialGroup, boolean) - Static method in class etomica.models.rowley.EthanolPotentialHelper
initPotential(ISpace, SpeciesMethanol, PotentialGroup, boolean, double, double) - Static method in class etomica.models.rowley.MethanolPotentialHelper
initPotential(ISpace, SpeciesMethanol, PotentialGroup) - Static method in class etomica.models.traPPE.MethanolPotentialHelper
initPotentials(ISimulation) - Method in class etomica.chem.models.Model: Internal method to be implemented by subclasses to initialize the intramolecular potentials associated with this model.
initPotentials(ISimulation) - Method in class etomica.chem.models.ModelChain
initRefPref(String, long) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
initRefPref(String, long) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
initRefPref(String, long, int) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlap
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapLJ
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapModule
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphere
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSSnxy
initRefPref(String, long) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
initRefPref(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
initRefPref(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
initU - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
initU - Variable in class etomica.models.nitrogen.MeterDirectInitPert
initVolume - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
initVolume - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
innersegment - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
inPlane(IVector) - Method in class etomica.lattice.LatticePlane: Returns true if the given point is inside the plane (within some small tolerance).
inPlane(IVector) - Method in class etomica.math.geometry.Plane: Returns true if the given point is within a distance epsilon of this plane.
inputFile - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
inputFile - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
inputFile - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
inputfilename - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
inRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
insert - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
insertCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
insertCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
inserted - Variable in class etomica.virial.MCMoveClusterAtomHSRing
inserted - Variable in class etomica.virial.MCMoveClusterAtomHSTree
inserted - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
Insertion - Class in etomica.modules.insertion
Insertion(Space) - Constructor for class etomica.modules.insertion.Insertion
insertion - Static variable in class org.jmol.script.Token
InsertionGraphic - Class in etomica.modules.insertion
InsertionGraphic(Insertion, Space) - Constructor for class etomica.modules.insertion.InsertionGraphic
InsertionGraphic.Applet - Class in etomica.modules.insertion
InsertionGraphic.MeterWidom - Class in etomica.modules.insertion
insertTransformerIfNeeded() - Method in class etomica.data.DataProcessor
INSTANCE - Static variable in class etomica.atom.iterator.AtomIteratorNull
INSTANCE - Static variable in class etomica.atom.iterator.IteratorFactory
INSTANCE - Static variable in class etomica.chem.elements.Argon
INSTANCE - Static variable in class etomica.chem.elements.Carbon
INSTANCE - Static variable in class etomica.chem.elements.Chlorine
INSTANCE - Static variable in class etomica.chem.elements.Copper
INSTANCE - Static variable in class etomica.chem.elements.Fluoride
INSTANCE - Static variable in class etomica.chem.elements.Helium
INSTANCE - Static variable in class etomica.chem.elements.Hydrogen
INSTANCE - Static variable in class etomica.chem.elements.Nitrogen
INSTANCE - Static variable in class etomica.chem.elements.Oxygen
INSTANCE - Static variable in class etomica.chem.elements.Silver
INSTANCE - Static variable in class etomica.chem.elements.Sodium
INSTANCE - Static variable in class etomica.chem.elements.Sulfur
INSTANCE - Static variable in class etomica.chem.elements.Tin
INSTANCE - Static variable in class etomica.chem.elements.Tungsten
INSTANCE - Static variable in class etomica.paracetamol.HydrogenP
INSTANCE - Static variable in class etomica.util.Function.Abs
INSTANCE - Static variable in class etomica.util.Function.Exp
INSTANCE - Static variable in class etomica.util.Function.Identity
INSTANCE - Static variable in class etomica.util.Function.Log
INSTANCE - Static variable in class etomica.util.Function.Reciprocal
INSTANCE - Static variable in class etomica.util.Function.Sqrt
Int - Class in etomica.graph.operations
Int() - Constructor for class etomica.graph.operations.Int
Int2IntHash - Class in org.jmol.util
Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
intArrayList - Variable in class etomica.data.AccumulatorAverageCollapsingLog
integer - Static variable in class org.jmol.script.Token
IntegerRange - Class in etomica.util
IntegerRange(int, int) - Constructor for class etomica.util.IntegerRange: Constructs the range defined by given values.
integral(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
integral(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
integral(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
integral(double) - Method in class etomica.potential.P2Ideal: Returns zero.
integral(double) - Method in class etomica.potential.P2LJQ
integral(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
integral(double) - Method in class etomica.potential.P2SoftTruncated: Returns the value of uInt for the wrapped potential.
integral(double) - Method in interface etomica.potential.Potential2Soft: Integral used to evaluate correction to truncation of potential.
integral(double) - Method in class etomica.potential.Potential2SoftSpherical: Same as uInt.
integrand(double) - Method in class etomica.statmech.HardSphere
integrate(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Replaces each cluster in the given array with another having the same topology, but with the highest-index root point converted into a field point.
integrator - Variable in class etomica.action.IntegratorActionAdapter
integrator - Variable in class etomica.AlkaneEH.CH4NVT
integrator - Variable in class etomica.AlkaneEH.DHS_NVT
integrator - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
integrator - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
integrator - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
integrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT
integrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
integrator - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
integrator - Variable in class etomica.data.DataProcessorChemicalPotential
integrator - Variable in class etomica.data.DataSourceCountCollisions
integrator - Variable in class etomica.data.DataSourceCountSteps
integrator - Variable in class etomica.data.DataSourceCountTime
integrator - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
integrator - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
integrator - Variable in class etomica.densityofstate.DensityOfState
integrator - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
integrator - Variable in class etomica.dielectric.DHS_NVT
integrator - Variable in class etomica.dielectric.DLJ_NVT_1site
integrator - Variable in class etomica.dielectric.TIP4P_NVT
integrator - Variable in class etomica.freeenergy.npath.SimIdealGas
integrator - Variable in class etomica.freeenergy.npath.SimLJ
integrator - Variable in class etomica.graphics.DisplayTimer
Integrator - Class in etomica.integrator: Integrator implements the algorithm used to move the atoms around and generate new configurations in one or more boxs.
Integrator() - Constructor for class etomica.integrator.Integrator
integrator - Variable in class etomica.integrator.IntegratorHard.Agent
integrator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
integrator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
integrator - Variable in class etomica.interfacial.LJMC
integrator - Variable in class etomica.interfacial.LJMD
integrator - Variable in class etomica.liquidLJ.LjMC3D
integrator - Variable in class etomica.liquidLJ.LjMd3D
integrator - Variable in class etomica.liquidLJ.LjMd3D.ValueCache
integrator - Variable in class etomica.liquidLJ.ValueCache
integrator - Variable in class etomica.mappedvirial.MappedU
integrator - Variable in class etomica.mappedvirial.MappedVirialLJ
integrator - Variable in class etomica.mappedvirial.MappedVirialLJVGr
integrator - Variable in class etomica.meam.EFSTungsten
integrator - Variable in class etomica.meam.MEAM_3DMDwithGB
integrator - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
integrator - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
integrator - Variable in class etomica.meam.MEAM_MC
integrator - Variable in class etomica.meam.MEAMMd3D
integrator - Variable in class etomica.metastable.LJmuVT
integrator - Variable in class etomica.metastable.LJNPT
integrator - Variable in class etomica.metastable.LJNVT
integrator - Variable in class etomica.models.hexane.HexaneVolumeFraction
integrator - Variable in class etomica.models.hexane.SimHarmonicHexane
integrator - Variable in class etomica.models.hexane.TestHexane
integrator - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
integrator - Variable in class etomica.models.hexane.TestHexaneFileConfig
integrator - Variable in class etomica.models.hexane.TestHexaneHarmonic
integrator - Variable in class etomica.models.hexane.TestSetToUHexane
integrator - Variable in class etomica.models.nitrogen.MeterBoltzmann
integrator - Variable in class etomica.models.nitrogen.MeterBoltzmannDirect
integrator - Variable in class etomica.models.nitrogen.MeterDirectInitPert
integrator - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
integrator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
integrator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
integrator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
integrator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
integrator - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
integrator - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
integrator - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
integrator - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
integrator - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
integrator - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
integrator - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
integrator - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
integrator - Variable in class etomica.models.oneDHardRods.SimWidomMode
integrator - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
integrator - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
integrator - Variable in class etomica.models.water.TestEwaldTIP4PWater
integrator - Variable in class etomica.modules.adsorption.ModifierPMu
integrator - Variable in class etomica.modules.adsorption.P1Wall
integrator - Variable in class etomica.modules.catalysis.Catalysis
integrator - Variable in class etomica.modules.colloid.ColloidSim
integrator - Variable in class etomica.modules.droplet.Droplet
integrator - Variable in class etomica.modules.droplet.DropletAtomic
integrator - Variable in class etomica.modules.ensembles.LJMC
integrator - Variable in class etomica.modules.entropylottery.EntropyLottery
integrator - Variable in class etomica.modules.insertion.Insertion
integrator - Variable in class etomica.modules.interfacial.InterfacialSW
integrator - Variable in class etomica.modules.ljmd.Ljmd
integrator - Variable in class etomica.modules.materialfracture.MaterialFracture
integrator - Variable in class etomica.modules.mu.Mu
integrator - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
integrator - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
integrator - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
integrator - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
integrator - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
integrator - Variable in class etomica.modules.osmosis.OsmosisSim
integrator - Variable in class etomica.modules.pistoncylinder.PistonCylinder
integrator - Variable in class etomica.modules.render.RenderMD: The Integrator performing the dynamics.
integrator - Variable in class etomica.modules.rheology.MeterNormalStress
integrator - Variable in class etomica.modules.rheology.MeterViscosity
integrator - Variable in class etomica.modules.rheology.SimulationRheology
integrator - Variable in class etomica.modules.rosmosis.MeterFlux
integrator - Variable in class etomica.modules.rosmosis.ReverseOsmosis
integrator - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
integrator - Variable in class etomica.modules.sam.Sam
integrator - Variable in class etomica.modules.swmd.Swmd
integrator - Variable in class etomica.normalmode.DeviceEigenvaluesSlider
integrator - Variable in class etomica.normalmode.DeviceWaveVectorSlider
integrator - Variable in class etomica.normalmode.HessianDB
integrator - Variable in class etomica.normalmode.HSDimerNPT
integrator - Variable in class etomica.normalmode.HSNPT
integrator - Variable in class etomica.normalmode.HTTPSoftSphereSim
integrator - Variable in class etomica.normalmode.MeterBoltzmann
integrator - Variable in class etomica.normalmode.MeterDirectSamplingTarget
integrator - Variable in class etomica.normalmode.MeterSamplingHarmonic
integrator - Variable in class etomica.normalmode.MeterSamplingTarget
integrator - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
integrator - Variable in class etomica.normalmode.MeterWorkBennetTarget
integrator - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
integrator - Variable in class etomica.normalmode.MeterWorkTargetBennet
integrator - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
integrator - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
integrator - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
integrator - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
integrator - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
integrator - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
integrator - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
integrator - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
integrator - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
integrator - Variable in class etomica.normalmode.SimBennet
integrator - Variable in class etomica.normalmode.SimCalcJ
integrator - Variable in class etomica.normalmode.SimCalcS
integrator - Variable in class etomica.normalmode.SimCalcSLJ
integrator - Variable in class etomica.normalmode.SimCalcSMorse
integrator - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
integrator - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
integrator - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
integrator - Variable in class etomica.normalmode.SimEinStep1
integrator - Variable in class etomica.normalmode.SimEinStep1HCP
integrator - Variable in class etomica.normalmode.SimEinStep2
integrator - Variable in class etomica.normalmode.SimEinStep2HCP
integrator - Variable in class etomica.normalmode.SimFluidSoftSphere
integrator - Variable in class etomica.normalmode.SimHarmonic
integrator - Variable in class etomica.normalmode.SimHarmonicUmbrella
integrator - Variable in class etomica.normalmode.SimHSMDVacancy
integrator - Variable in class etomica.normalmode.SimLJHTTISuper
integrator - Variable in class etomica.normalmode.SimLJHTTISuperHCP
integrator - Variable in class etomica.normalmode.SimLJVacancy
integrator - Variable in class etomica.normalmode.SimModesJ
integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
integrator - Variable in class etomica.normalmode.SimTarget
integrator - Variable in class etomica.normalmode.SimTargetUmbrella
integrator - Variable in class etomica.normalmode.SimUmbrella
integrator - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
integrator - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
integrator - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
integrator - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
integrator - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
integrator - Variable in class etomica.paracetamol.MDParacetamolMonoclinic: The Integrator performing the dynamics.
integrator - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic: The Integrator performing the dynamics.
integrator - Variable in class etomica.potential.PotentialCalculationPressureTensor
integrator - Variable in class etomica.rotation.DipoleBox
integrator - Variable in class etomica.rotation.DipoleBoxMatrix
integrator - Variable in class etomica.simulation.prototypes.ChainHSMD3D
integrator - Variable in class etomica.simulation.prototypes.GEMCWithRotation
integrator - Variable in class etomica.simulation.prototypes.HsMc2d
integrator - Variable in class etomica.simulation.prototypes.HSMD2D
integrator - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
integrator - Variable in class etomica.simulation.prototypes.HSMD3D: The Integrator performing the dynamics.
integrator - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
integrator - Variable in class etomica.simulation.prototypes.LjMd2D
integrator - Variable in class etomica.simulation.prototypes.LjMd3D
integrator - Variable in class etomica.simulation.prototypes.SoftSphere3d
integrator - Variable in class etomica.simulation.prototypes.SwMd2D
integrator - Variable in class etomica.simulation.prototypes.SWMD3D
integrator - Variable in class etomica.surfacetension.LJMC
integrator - Variable in class etomica.tests.TestHSMD3D
integrator - Variable in class etomica.tests.TestLJMC3D
integrator - Variable in class etomica.tests.TestSWChain
integrator - Variable in class etomica.thermointegration.LjMc3D
integrator - Variable in class etomica.threaded.atom.LJMD3DThreaded
integrator - Variable in class etomica.threaded.domain.LJMD3DThreaded
integrator - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
integrator - Variable in class etomica.virial.simulations.ModifierTPI
integrator - Variable in class etomica.virial.simulations.SimulationVirial
integrator - Variable in class etomica.virial.simulations.SimulationVirialPT
integrator - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
integrator - Variable in class etomica.yukawa.TestHC2YukawaMC3D
integrator - Variable in class etomica.yukawa.TestYukawaMC3D
integrator - Variable in class etomica.yukawa.TestYukawaMD3D
integrator - Variable in class etomica.zeolite.ZeoliteSimulation: The Integrator performing the dynamics.
Integrator.Forcible - Interface in etomica.integrator: Integrator agent that holds a force vector.
Integrator.Torquable - Interface in etomica.integrator: Integrator agent that holds a torque vector.
integrator1 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
integrator1 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
integrator2 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
integrator2 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
integratorA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
integratorA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
integratorA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
integratorA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
IntegratorAction - Interface in etomica.action: Elementary action performed on an integrator.
IntegratorActionAdapter - Class in etomica.action: Convenience class used to define a IntegratorAction.
IntegratorActionAdapter() - Constructor for class etomica.action.IntegratorActionAdapter
IntegratorActionAdapter(IIntegrator) - Constructor for class etomica.action.IntegratorActionAdapter: Constructs the Action with the given descriptive label.
integratorAgentManager - Variable in class etomica.potential.PotentialCalculationForceSum
IntegratorAnalytic - Class in etomica.integrator: Integrator that generates atom trajectories from an analytic formula.
IntegratorAnalytic(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorAnalytic
IntegratorAnalytic(IPotentialMaster, IRandom, double, ISpace) - Constructor for class etomica.integrator.IntegratorAnalytic
IntegratorAnalytic.AtomTimeAction - Class in etomica.integrator: Extends AtomAction class to add a method to set the time.
integratorB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
integratorB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
integratorB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
integratorB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
IntegratorBox - Class in etomica.integrator: Integrator implements the algorithm used to move the atoms around and generate new configurations in one or more boxs.
IntegratorBox(IPotentialMaster, double) - Constructor for class etomica.integrator.IntegratorBox
IntegratorConNVT - Class in etomica.integrator: Constant NVT Molecular Dynamics Integrator-Constraint Method Uses a modified version of the Leap Frog Algorithm.
IntegratorConNVT(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorConNVT
IntegratorConNVT(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorConNVT
IntegratorConNVT.Agent - Class in etomica.integrator
integratorDCV - Variable in class etomica.modules.dcvgcmd.DCVGCMD
IntegratorDCVGCMD - Class in etomica.modules.dcvgcmd
IntegratorDCVGCMD(IPotentialMaster, double, ISpace, ISpecies, ISpecies) - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD
IntegratorDCVGCMD.Mu1Modulator - Class in etomica.modules.dcvgcmd
IntegratorDCVGCMD.Mu2Modulator - Class in etomica.modules.dcvgcmd
integratorDimer - Variable in class etomica.dimer.SimDimerLJadatom
integratorDimer - Variable in class etomica.dimer.SimDimerLJgb
integratorDimer - Variable in class etomica.dimer.SimDimerMEAMadatom
integratorDimer - Variable in class etomica.dimer.SimDimerMEAMGB
integratorDimer - Variable in class etomica.kmc.SimKMCLJadatom
integratorDimer - Variable in class etomica.kmc.SimKMCMEAMadatom
IntegratorDimerApproach - Class in etomica.action
IntegratorDimerApproach(IPotentialMaster, ISpace) - Constructor for class etomica.action.IntegratorDimerApproach
IntegratorDimerMin - Class in etomica.dimer: Henkelman's Dimer Method (Minimum Energy Path).
IntegratorDimerMin(ISimulation, IPotentialMaster, ISpecies[], Boolean, ISpace) - Constructor for class etomica.dimer.IntegratorDimerMin
IntegratorDimerMin(ISimulation, IPotentialMaster, double, ISpecies[], Boolean, ISpace) - Constructor for class etomica.dimer.IntegratorDimerMin
integratorDimerMin - Variable in class etomica.dimer.SimDimerLJadatom
integratorDimerMin - Variable in class etomica.dimer.SimDimerMEAMadatom
integratorDimerMin - Variable in class etomica.dimer.SimDimerMEAMGB
IntegratorDimerRT - Class in etomica.dimer: Henkelman's Dimer Method (Rotation and Translation).
IntegratorDimerRT(ISimulation, IPotentialMaster, ISpecies[], ISpace) - Constructor for class etomica.dimer.IntegratorDimerRT
IntegratorDimerRT(ISimulation, IPotentialMaster, IRandom, double, ISpecies[], ISpace) - Constructor for class etomica.dimer.IntegratorDimerRT
IntegratorDroplet - Class in etomica.modules.droplet: Mesoscale integrator for Droplet module.
IntegratorDroplet(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.modules.droplet.IntegratorDroplet
IntegratorDroplet(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.modules.droplet.IntegratorDroplet
IntegratorDroplet.MyAgent - Class in etomica.modules.droplet
IntegratorEnergyMap - Class in etomica.dimer
IntegratorEnergyMap(ISimulation, PotentialMaster, IAtom, String, ISpace) - Constructor for class etomica.dimer.IntegratorEnergyMap
IntegratorEvent - Class in etomica.integrator: Event object given to registered listeners when an integrator fires any type event.
IntegratorEvent(IIntegrator, IntegratorEvent.Type) - Constructor for class etomica.integrator.IntegratorEvent
IntegratorEvent.Type - Class in etomica.integrator
IntegratorEventManager - Class in etomica.integrator
IntegratorEventManager() - Constructor for class etomica.integrator.IntegratorEventManager
IntegratorFixedWall - Class in etomica.interfacial
IntegratorFixedWall(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.interfacial.IntegratorFixedWall
integratorForceComputed(IIntegratorEvent) - Method in interface etomica.api.IIntegratorListenerMD: Invoked after the integrator has computed the forces on all atoms in the system.
integratorForceComputed(IIntegratorEvent) - Method in class etomica.interfacial.FixedWall
IntegratorGear4 - Class in etomica.integrator: Gear 4th-order predictor-corrector integrator.
IntegratorGear4(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorGear4
IntegratorGear4(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorGear4
IntegratorGear4.Agent - Class in etomica.integrator
IntegratorGear4NPH - Class in etomica.integrator: Gear 4th-order predictor-corrector integrator for constant enthalphy, pressure.
IntegratorGear4NPH(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorGear4NPH
IntegratorGear4NPH(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorGear4NPH
IntegratorGear4NPH.EnsembleToggler - Class in etomica.integrator
IntegratorGear4NPH.ForceSumNPH - Class in etomica.integrator
IntegratorGear4NPH.MeterEnthalpy - Class in etomica.integrator
IntegratorGEMC - Class in etomica.integrator: Simple Gibbs-ensemble Monte Carlo integrator.
IntegratorGEMC(IRandom, ISpace) - Constructor for class etomica.integrator.IntegratorGEMC
integratorGEMC - Variable in class etomica.modules.vle.VLESim
integratorHard - Variable in class etomica.data.DataSourceTensorVirialHard
integratorHard - Variable in class etomica.data.meter.MeterPressureHard
IntegratorHard - Class in etomica.integrator: Integrator for hard potentials.
IntegratorHard(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorHard
IntegratorHard(ISimulation, IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorHard
integratorHard - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
integratorHard - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
integratorHard - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
integratorHard - Variable in class etomica.modules.mu.DataSourceWallPressureMu
IntegratorHard.Agent - Class in etomica.integrator: Agent defined by this integrator.
IntegratorHard.CollisionHandlerUp - Class in etomica.integrator
IntegratorHard.CollisionListener - Interface in etomica.integrator
integratorHard1 - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
IntegratorHardMDMC - Class in etomica.normalmode: Custom DMD integrator that handles hybrid simulations with insertion/deletions.
IntegratorHardMDMC(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.normalmode.IntegratorHardMDMC
IntegratorHardPiston - Class in etomica.modules.pistoncylinder: Integrator for DMD with a piston (P1HardMovingBoundary)
IntegratorHardPiston(ISimulation, IPotentialMaster, P1HardMovingBoundary, ISpace) - Constructor for class etomica.modules.pistoncylinder.IntegratorHardPiston
integratorHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
IntegratorHarmonic - Class in etomica.normalmode: Integrator that is used for the harmonic osciallating system
IntegratorHarmonic(IRandom, double, double, ISpace) - Constructor for class etomica.normalmode.IntegratorHarmonic
integratorHybrid - Variable in class etomica.modules.adsorption.Adsorption
IntegratorHybrid - Class in etomica.modules.adsorption
IntegratorHybrid(PotentialMasterHybrid, IntegratorMD, IntegratorMC, double) - Constructor for class etomica.modules.adsorption.IntegratorHybrid
integratorInitialized(IIntegratorEvent) - Method in interface etomica.api.IIntegratorListener: Invoked when integration begins.
integratorInitialized(IIntegratorEvent) - Method in class etomica.data.DataPumpListener
integratorInitialized(IIntegratorEvent) - Method in class etomica.data.DataPumpListenerPow
integratorInitialized(IIntegratorEvent) - Method in class etomica.data.DataPumpListenerPowStrict
integratorInitialized(IIntegratorEvent) - Method in class etomica.interfacial.FixedWall
integratorInitialized(IIntegratorEvent) - Method in class etomica.listener.IntegratorListenerAction
integratorInitialized(IIntegratorEvent) - Method in class etomica.listener.IntegratorListenerGroupSeries
integratorInitialized(IIntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
integratorInitialized(IIntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
integratorInitialized(IIntegratorEvent) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
integratorInitialized(IIntegratorEvent) - Method in class etomica.nbr.list.NeighborListManager
IntegratorJT - Class in etomica.modules.joulethomson
IntegratorJT(IRandom, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.joulethomson.IntegratorJT
IntegratorJT.EnsembleToggler - Class in etomica.modules.joulethomson
IntegratorKMC - Class in etomica.kmc
IntegratorKMC(ISimulation, IPotentialMaster, double, IRandom, ISpecies[], ISpace) - Constructor for class etomica.kmc.IntegratorKMC
integratorKMC - Variable in class etomica.kmc.SimKMCLJadatom
integratorKMC() - Method in class etomica.kmc.SimKMCLJadatom
integratorKMC - Variable in class etomica.kmc.SimKMCMEAMadatom
integratorKMC() - Method in class etomica.kmc.SimKMCMEAMadatom
IntegratorKMCCluster - Class in etomica.kmc
IntegratorKMCCluster(ISimulation, IPotentialMaster, double, int, IRandom, ISpecies[], ISpace) - Constructor for class etomica.kmc.IntegratorKMCCluster
integratorKMCCluster - Variable in class etomica.kmc.SimKMCLJadatom
integratorKMCCluster(double, int, int) - Method in class etomica.kmc.SimKMCLJadatom
integratorKMCCluster - Variable in class etomica.kmc.SimKMCMEAMadatom
integratorKMCCluster(double, int, int) - Method in class etomica.kmc.SimKMCMEAMadatom
integratorLiquid - Variable in class etomica.modules.vle.VLESim
IntegratorListenerAction - Class in etomica.listener
IntegratorListenerAction(IAction) - Constructor for class etomica.listener.IntegratorListenerAction
IntegratorListenerAction(IAction, int) - Constructor for class etomica.listener.IntegratorListenerAction
IntegratorListenerGroupSeries - Class in etomica.listener
IntegratorListenerGroupSeries() - Constructor for class etomica.listener.IntegratorListenerGroupSeries: Constructs an action group that holds no actions.
IntegratorListenerGroupSeries(IIntegratorListener[]) - Constructor for class etomica.listener.IntegratorListenerGroupSeries: Defines group via the given array of actions.
IntegratorManagerMC - Class in etomica.integrator: Integrator manages other Integrators which either act on a Box, or manage still other Integrators.
IntegratorManagerMC(IRandom) - Constructor for class etomica.integrator.IntegratorManagerMC
integratorMAP - Variable in class etomica.dimer.EnergyMap
IntegratorMC - Class in etomica.integrator: Integrator to perform Metropolis Monte Carlo sampling.
IntegratorMC(ISimulation, IPotentialMaster) - Constructor for class etomica.integrator.IntegratorMC
IntegratorMC(IPotentialMaster, IRandom, double) - Constructor for class etomica.integrator.IntegratorMC: Constructs integrator and establishes PotentialMaster instance that will be used by moves to calculate the energy.
integratorMC - Variable in class etomica.integrator.IntegratorMD
integratorMC - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
integratorMC - Variable in class etomica.liquidLJ.LjMd3D
integratorMC - Variable in class etomica.modules.adsorption.Adsorption
integratorMC - Variable in class etomica.modules.adsorption.IntegratorHybrid
integratorMC - Variable in class etomica.normalmode.SimHSMDVacancy
integratorMD - Variable in class etomica.dimer.SimDimerLJadatom
integratorMD - Variable in class etomica.dimer.SimDimerLJgb
integratorMD - Variable in class etomica.dimer.SimDimerMEAMadatom
integratorMD - Variable in class etomica.dimer.SimDimerMEAMGB
IntegratorMD - Class in etomica.integrator: Superclass of all molecular-dynamics integrators.
IntegratorMD(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorMD
integratorMD - Variable in class etomica.modules.adsorption.Adsorption
integratorMD - Variable in class etomica.modules.adsorption.IntegratorHybrid
IntegratorMD.ThermostatType - Class in etomica.integrator
IntegratorMD.VectorSource - Class in etomica.integrator
IntegratorNonintervalEvent - Class in etomica.integrator: Event thrown by integrator when it announces reaching special points in the simulation process, such as its beginning and end.
IntegratorNonintervalEvent(IIntegrator, IntegratorNonintervalEvent.NonintervalEventType) - Constructor for class etomica.integrator.IntegratorNonintervalEvent
IntegratorNonintervalEvent.NonintervalEventType - Class in etomica.integrator
integratorOS - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
integratorOS - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
integratorOS - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
integratorOS - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
integratorOS - Variable in class etomica.virial.simulations.SimulationVirialOverlap
integratorOS - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
integratorOverlap - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
integratorOverlap - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
integratorOverlap - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
integratorOverlap - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
integratorOverlap - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
integratorOverlap - Variable in class etomica.normalmode.SimOverlap
integratorOverlap - Variable in class etomica.normalmode.SimOverlapLJ
integratorOverlap - Variable in class etomica.normalmode.SimOverlapLJModule
integratorOverlap - Variable in class etomica.normalmode.SimOverlapModule
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphere
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
integratorOverlap - Variable in class etomica.normalmode.SimOverlapSSnxy
IntegratorOverlap - Class in etomica.overlap: This integrator class manages (2) sub-integrators for an overlap sampling simulation.
IntegratorOverlap(IIntegrator[]) - Constructor for class etomica.overlap.IntegratorOverlap
IntegratorOverlap - Class in etomica.virial.overlap: This integrator class manages (2) sub-integrators for an overlap sampling simulation.
IntegratorOverlap(IIntegrator[]) - Constructor for class etomica.virial.overlap.IntegratorOverlap
IntegratorOverlap.ReferenceFracSource - Interface in etomica.overlap
IntegratorPolymer - Class in etomica.modules.rheology: Integrator for Brownian dynamics of a polymer in a flow field.
IntegratorPolymer(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.modules.rheology.IntegratorPolymer
IntegratorPT - Class in etomica.integrator: Parallel-tempering integrator.
IntegratorPT(IRandom, ISpace) - Constructor for class etomica.integrator.IntegratorPT
IntegratorPT(IRandom, IntegratorPT.MCMoveSwapFactory, ISpace) - Constructor for class etomica.integrator.IntegratorPT
integratorPT - Variable in class etomica.virial.simulations.SimulationVirialPT
IntegratorPT.BoxTracker - Class in etomica.integrator: Meter that tracks the swapping of the boxes in parallel-tempering simulation.
IntegratorPT.MCMoveSwap - Interface in etomica.integrator: Interface for a move that swaps two boxes.
IntegratorPT.MCMoveSwapFactory - Interface in etomica.integrator: Interface for a class that can make a MCMove that will swap the configurations of two boxes.
IntegratorReset - Class in etomica.action: Action that calls the reset method of an integrator.
IntegratorReset() - Constructor for class etomica.action.IntegratorReset
IntegratorReset(IIntegrator, boolean) - Constructor for class etomica.action.IntegratorReset
IntegratorRigidIterative - Class in etomica.integrator
IntegratorRigidIterative(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorRigidIterative
IntegratorRigidIterative(ISimulation, IPotentialMaster, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorRigidIterative
IntegratorRigidIterative.MoleculeAgent - Class in etomica.integrator
IntegratorRigidMatrixIterative - Class in etomica.integrator: Integrator implementation of Omelyan's leapfrog integrator for rotational motion.
IntegratorRigidMatrixIterative(ISimulation, PotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative
IntegratorRigidMatrixIterative(ISimulation, PotentialMaster, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative
IntegratorRigidMatrixIterative.AtomAgent - Class in etomica.integrator
IntegratorRigidMatrixIterative.BoxImposePbcMolecule - Class in etomica.integrator
IntegratorRigidMatrixIterative.MoleculeAgent - Class in etomica.integrator
integrators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
integrators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
integrators - Variable in class etomica.integrator.IntegratorManagerMC
integrators - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
integrators - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
integrators - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
integrators - Variable in class etomica.normalmode.SimOverlap
integrators - Variable in class etomica.normalmode.SimOverlapLJ
integrators - Variable in class etomica.normalmode.SimOverlapLJModule
integrators - Variable in class etomica.normalmode.SimOverlapModule
integrators - Variable in class etomica.normalmode.SimOverlapSoftSphere
integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
integrators - Variable in class etomica.normalmode.SimOverlapSSnxy
integrators - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
integrators - Variable in class etomica.virial.simulations.SimulationVirialOverlap
integrators - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImage
integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
integratorSim - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
integratorSim - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
IntegratorSmoother(AkimaSplineSmoother) - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp.IntegratorSmoother
IntegratorSmoother(AkimaSplineSmoother) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp.IntegratorSmoother
integratorStepFinished(IIntegratorEvent) - Method in interface etomica.api.IIntegratorListener: Invoked at the end of each integrator step.
integratorStepFinished(IIntegratorEvent) - Method in class etomica.data.DataPumpListener
integratorStepFinished(IIntegratorEvent) - Method in class etomica.data.DataPumpListenerPow
integratorStepFinished(IIntegratorEvent) - Method in class etomica.data.DataPumpListenerPowStrict
integratorStepFinished(IIntegratorEvent) - Method in class etomica.interfacial.FixedWall
integratorStepFinished(IIntegratorEvent) - Method in class etomica.listener.IntegratorListenerAction
integratorStepFinished(IIntegratorEvent) - Method in class etomica.listener.IntegratorListenerGroupSeries
integratorStepFinished(IIntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
integratorStepFinished(IIntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
integratorStepFinished(IIntegratorEvent) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
integratorStepFinished(IIntegratorEvent) - Method in class etomica.nbr.list.NeighborListManager
integratorStepStarted(IIntegratorEvent) - Method in interface etomica.api.IIntegratorListener: Invoked at the beginning of each integrator step.
integratorStepStarted(IIntegratorEvent) - Method in class etomica.data.DataPumpListener
integratorStepStarted(IIntegratorEvent) - Method in class etomica.data.DataPumpListenerPow
integratorStepStarted(IIntegratorEvent) - Method in class etomica.data.DataPumpListenerPowStrict
integratorStepStarted(IIntegratorEvent) - Method in class etomica.interfacial.FixedWall
integratorStepStarted(IIntegratorEvent) - Method in class etomica.listener.IntegratorListenerAction
integratorStepStarted(IIntegratorEvent) - Method in class etomica.listener.IntegratorListenerGroupSeries
integratorStepStarted(IIntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
integratorStepStarted(IIntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
integratorStepStarted(IIntegratorEvent) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
integratorStepStarted(IIntegratorEvent) - Method in class etomica.nbr.list.NeighborListManager
integratorTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
integratorTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
integratorTarget - Variable in class etomica.normalmode.SimOverlap
IntegratorThermodynamic - Class in etomica.thermointegration: Abstract class suitable as a parent class for thermodynamic integration integrators.
IntegratorThermodynamic(IIntegrator) - Constructor for class etomica.thermointegration.IntegratorThermodynamic: Constructs a thermodynamic integrator that operates with the given sub integrator, which is responsible for exploring configruations at any given state point.
IntegratorThermodynamicPEvsT - Class in etomica.thermointegration
IntegratorThermodynamicPEvsT(IntegratorBox) - Constructor for class etomica.thermointegration.IntegratorThermodynamicPEvsT
IntegratorTMMC - Class in etomica.tmmc: Integrator that implements Transition-Matrix Monte Carlo method.
IntegratorTMMC(ISimulation, IPotentialMaster) - Constructor for class etomica.tmmc.IntegratorTMMC
IntegratorTMMC(IPotentialMaster, IRandom, double) - Constructor for class etomica.tmmc.IntegratorTMMC
integratorVapor - Variable in class etomica.modules.vle.VLESim
IntegratorVelocityVerlet - Class in etomica.integrator
IntegratorVelocityVerlet(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerlet
IntegratorVelocityVerlet(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerlet
IntegratorVelocityVerlet.MyAgent - Class in etomica.integrator
IntegratorVelocityVerletQuaternion - Class in etomica.rotation
IntegratorVelocityVerletQuaternion(ISimulation, PotentialMaster, Space) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion
IntegratorVelocityVerletQuaternion(ISimulation, PotentialMaster, double, double, Space) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion
IntegratorVelocityVerletQuaternion.AtomAgent - Class in etomica.rotation
IntegratorVelocityVerletQuaternion.MoleculeAgent - Class in etomica.rotation
IntegratorVelocityVerletQuaternion.MyTypeAgent - Class in etomica.rotation
IntegratorVelocityVerletRattle - Class in etomica.integrator: Integrator implementing RATTLE algorithm.
IntegratorVelocityVerletRattle(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerletRattle
IntegratorVelocityVerletRattle(ISimulation, IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerletRattle
IntegratorVelocityVerletSAM - Class in etomica.modules.sam: Special integrator subclass that has the ability to prevent sulfur atoms from moving in the Y direction.
IntegratorVelocityVerletSAM(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.modules.sam.IntegratorVelocityVerletSAM
IntegratorVelocityVerletShake - Class in etomica.integrator: Integrator implementing SHAKE algorithm.
IntegratorVelocityVerletShake(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake
IntegratorVelocityVerletShake(ISimulation, IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake
IntegratorVelocityVerletShake.BondConstraints - Class in etomica.integrator
IntegratorVelocityVerletThreaded - Class in etomica.threaded
IntegratorVelocityVerletThreaded(IRandom, ISpace, IPotentialMaster, int) - Constructor for class etomica.threaded.IntegratorVelocityVerletThreaded
IntegratorVelocityVerletThreaded(IPotentialMaster, IRandom, double, double, int, ISpace) - Constructor for class etomica.threaded.IntegratorVelocityVerletThreaded
IntegratorVerlet - Class in etomica.integrator
IntegratorVerlet(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.IntegratorVerlet
IntegratorVerlet(IPotentialMaster, IRandom, double, double, ISpace) - Constructor for class etomica.integrator.IntegratorVerlet
IntegratorVerlet.Agent - Class in etomica.integrator
intenseFraction - Static variable in class org.jmol.util.Shader
interactionAgentManager - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityCO
interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityCO2
interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityO2
interactionRange - Variable in class etomica.nbr.CriterionSimple
interactionRange - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
interactionTracker - Variable in class etomica.modules.catalysis.Catalysis
InteractionTracker - Class in etomica.modules.catalysis
InteractionTracker(IBox, ISpecies) - Constructor for class etomica.modules.catalysis.InteractionTracker
InteractionTracker.CatalysisAgent - Class in etomica.modules.catalysis
InterfacialSW - Class in etomica.modules.interfacial: Simulation for interfacial tension module.
InterfacialSW(Space) - Constructor for class etomica.modules.interfacial.InterfacialSW
InterfacialSWGraphic - Class in etomica.modules.interfacial: Graphic UI for interfacial tension module.
InterfacialSWGraphic(InterfacialSW, Space) - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic
InterfacialSWGraphic.Applet - Class in etomica.modules.interfacial
InterfacialSWGraphic.DataProcessorTensorSplitter - Class in etomica.modules.interfacial: Inner class to find the total pressure of the system from the pressure tensor.
InterfacialSWGraphic.ModifierBoxSize - Class in etomica.modules.interfacial
interiorColor - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
intermolecular - Static variable in class org.jmol.script.Token
interpolatedDy - Variable in class etomica.util.numerical.AkimaSpline
interpolatedY - Variable in class etomica.util.numerical.AkimaSpline
interPotential - Variable in class etomica.parser.ParserLAMMPS.Stuff
Interpreter - Class in etomica.graph.engine
Interpreter(ConsoleContainer, Environment, Parser) - Constructor for class etomica.graph.engine.Interpreter
Interpreter.InterpreterException - Exception in etomica.graph.engine
InterpreterException(String) - Constructor for exception etomica.graph.engine.Interpreter.InterpreterException
InterpreterException(String, Throwable) - Constructor for exception etomica.graph.engine.Interpreter.InterpreterException
intersectPlane(Point4f, float, int) - Method in class org.jmol.util.BoxInfo: returns a set of points defining the geometric object within the given plane that spans the unit cell within the given margins
intersectPlane(Point4f, List<Object>, int) - Static method in class org.jmol.util.TriangleData: a generic cell - plane intersector -- used for finding the plane through a unit cell
intersects(BitSet) - Method in class org.jmol.util.BitSet: Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.
interType - Variable in class etomica.potential.Potential0Lrc
interval - Variable in class etomica.data.DataPumpListener
interval - Variable in class etomica.data.DataPumpListenerPow
interval - Variable in class etomica.data.DataPumpListenerPowStrict
interval - Variable in class etomica.integrator.Integrator
interval - Variable in class etomica.util.HistoryCollapsing
intervalCount - Variable in class etomica.data.DataPumpListener
intervalCount - Variable in class etomica.data.DataPumpListenerPowStrict
intervalCount - Variable in class etomica.util.HistoryCollapsing
intervalListeners - Variable in class etomica.integrator.IntegratorEventManager
intervals - Variable in class etomica.data.DataPumpListenerPow
intKeySelect(char) - Static method in class etomica.units.Prefix: Returns an integer code corresponding to the prefix for the given key.
intoTruncatedOctahedron - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
intparam - Static variable in class org.jmol.script.Token
IntParameters - Class in etomica.graph.operations
IntParameters(byte) - Constructor for class etomica.graph.operations.IntParameters
intproperty - Static variable in class org.jmol.script.Token
intraAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
intramolecular - Static variable in class org.jmol.script.Token
intraPotential - Variable in class etomica.parser.ParserLAMMPS.Stuff
intraPotentialIterator - Variable in class etomica.nbr.PotentialMasterNbr
introspect(Object, String, BeanInfo) - Static method in class etomica.units.Dimension: Method to determine the dimension of a property via introspection.
IntSet - Class in etomica.virial: An IntSet holds an array of integers and can act as a has key.
IntSet(int[]) - Constructor for class etomica.virial.IntSet
IntSet.PropertyBin - Interface in etomica.virial
intToken(int) - Static method in class org.jmol.script.Token
intValue - Variable in class org.jmol.script.Token
inv() - Method in class org.jmol.util.Quaternion
invalidatePolygons() - Method in class org.jmol.util.MeshSurface
inverse() - Method in class etomica.math.Quaternion: Returns the inverse of the Quaternion q given by q^-1 = 1/(norm^2) * q*
inverse(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
inverse(double) - Method in class etomica.util.Function.Exp
inverse(double) - Method in class etomica.util.Function.Identity
inverse(double) - Method in class etomica.util.Function.Linear
inverse(double) - Method in class etomica.util.Function.Log
inverse(double) - Method in class etomica.util.Function.Reciprocal
inverse(double) - Method in class etomica.util.Function.Sqrt
inverse(double) - Method in class etomica.util.FunctionChain: Inverts function by calling inverse methods of subfunctions, in reverse order of their addition.
inverse(double) - Method in interface etomica.util.FunctionInvertible
inverseProduct3D(IVectorMutable, IVector, IVector) - Method in class etomica.potential.P2SpheroPolyhedron
inverseProduct4D(IVectorMutable, IVector, IVector) - Method in class etomica.potential.P2SpheroPolyhedron
invert() - Method in class etomica.lattice.LatticePlane: Changes the direction of the normal vector so that it points toward the other side of the plane from its present orientation.
invert() - Method in class etomica.math.geometry.Plane: Changes the direction of the normal vector so that it points toward the other side of the plane from its present orientation.
invert() - Method in interface etomica.space.Tensor
invert() - Method in class etomica.space1d.Tensor1D
invert() - Method in class etomica.space2d.Tensor2D
invert() - Method in class etomica.space3d.RotationTensor3D
invert() - Method in class etomica.space3d.Tensor3D
invert() - Method in class etomica.spaceNd.TensorND
invert() - Method in class etomica.util.FastFourierTransform: Reverse Transformation of discrete data sets
invert() - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to its inverse.
invert() - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to its inverse.
invertInPlace(BitSet, int) - Static method in class org.jmol.util.BitSetUtil: inverts the bitset bits 0 through n-1, and returns a reference to the modified bitset
invertM(Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the matrix inverse of the passed matrix m1.
invertM(Matrix4f) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to the matrix inverse of the passed matrix m1.
invertRound(BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Build the inverse and maintain the approximate accuracy.
ionic - Static variable in class org.jmol.script.Token
iopt - Static variable in class etomica.potential.P2WaterPotentialsJankowski
iOrientation - Variable in class etomica.atom.AtomOriented
iOrientation - Variable in class etomica.atom.AtomOrientedDynamic
IOrientation - Interface in etomica.space: Interface for a class that specifies an orientation in space.
IOrientation2D - Interface in etomica.space2d: Interface for a class that specifies an orientation in a 2D space.
IOrientation3D - Interface in etomica.space3d: Interface for an orientation in 3D.
IOrientationFull3D - Interface in etomica.space3d: Interface representing an orientation in 3D.
iparams - Static variable in class etomica.models.co2.P2CO2H2OWheatley
iPosition - Variable in class etomica.virial.CoordinatePairMoleculeSet
IPotential - Interface in etomica.api
IPotential0Lrc - Interface in etomica.potential: Interface for a long-range correction potential.
IPotential0MoleculeLrc - Interface in etomica.potential: Interface for a long-range correction potential.
IPotentialAtomic - Interface in etomica.api
IPotentialAtomicMultibody - Interface in etomica.potential: Interface for an atomic non-additive potential.
IPotentialCalculationThreaded - Interface in etomica.threaded
IPotentialCalculationWallForce - Interface in etomica.modules.rosmosis
IPotentialMaster - Interface in etomica.api
IPotentialMolecular - Interface in etomica.api
IPotentialMolecularSecondDerivative - Interface in etomica.potential
IPotentialMolecularTorque - Interface in etomica.potential
IPotentialTorque - Interface in etomica.potential
iPotParts - Static variable in class etomica.potential.P2WaterPotentialsJankowski
ipr - Static variable in class etomica.potential.P2WaterPotentialsJankowski
iRand - Variable in class etomica.normalmode.MCMoveHarmonic
IRandom - Interface in etomica.api: Interface for random number generation.
iroots() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Generate the integer roots of the polynomial.
irpowex - Static variable in class etomica.potential.P2HydrogenPatkowski
irpowex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
irpowsp - Static variable in class etomica.potential.P2HydrogenPatkowski
irpowsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
is864 - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
is864() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
IS_EMPTY - Static variable in class etomica.compatibility.Feature
IS_EQUAL - Static variable in class etomica.compatibility.Feature
isAB(Object) - Static method in class org.jmol.util.Escape
isAccepted() - Method in class etomica.integrator.mcmove.MCMoveTrialCompletedEvent
isActive - Variable in class etomica.action.Activity
isActive() - Method in class etomica.action.Activity: Indicates if the integrator has been started and has not yet completed.
isActive() - Method in class etomica.data.DataAccumulator: Indicates whether accumulation is being performed in response to interval events.
isActiveLevel(int) - Static method in class org.jmol.util.Logger: Tells if a logging level is active.
isAD(Object) - Static method in class org.jmol.util.Escape
isAdiabatic() - Method in class etomica.graphics.DeviceThermoSlider
isAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
isAdjustStepFraction() - Method in class etomica.overlap.IntegratorOverlap: Sets whether to adjust the number of relative number of steps for each sub-integrator.
isAdjustStepFreq() - Method in class etomica.virial.overlap.IntegratorOverlap: Sets whether to adjust the number of relative number of steps for each sub-integrator.
isAF(Object) - Static method in class org.jmol.util.Escape
isAFF(Object) - Static method in class org.jmol.util.Escape
isAFFF(Object) - Static method in class org.jmol.util.Escape
isAFloat(Object) - Static method in class org.jmol.util.Escape
isAI(Object) - Static method in class org.jmol.util.Escape
isAII(Object) - Static method in class org.jmol.util.Escape
isAllEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
isAllowEqualElements() - Method in class etomica.lattice.IndexIteratorTriangular
isAllWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
isAlpha - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
isAlpha - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
isAntialiased() - Method in class org.jmol.util.GData: is full scene / oversampling antialiasing in effect
isAP(Object) - Static method in class org.jmol.util.Escape
isAppend() - Method in class etomica.action.XYZWriter
isAppending() - Method in class etomica.data.DataLogger
isApplyToMolecules() - Method in class etomica.action.BoxImposePbc: Returns the value of applyToMolecules.
isaromatic - Static variable in class org.jmol.script.Token
isArticulated(Graph, int, int) - Method in class etomica.graph.property.FactorFFT
IsArticulationPair - Class in etomica.graph.property
IsArticulationPair() - Constructor for class etomica.graph.property.IsArticulationPair
isArticulationPair(Graph, int, int) - Method in class etomica.graph.property.IsArticulationPair
isArticulationPair(int, int) - Method in class etomica.virial.cluster.ClusterGenerator: determines if the given pair of points is an articulation pair.
IsArticulationPoint - Class in etomica.graph.property
IsArticulationPoint() - Constructor for class etomica.graph.property.IsArticulationPoint
isArticulationPoint(Graph, int) - Method in class etomica.graph.property.IsArticulationPoint
isArticulationPoint(int) - Method in class etomica.virial.cluster.ClusterGenerator: Determines if the given point is an articulation point.
isAS(Object) - Static method in class org.jmol.util.Escape
isASS(Object) - Static method in class org.jmol.util.Escape
isAssociated(IAtom, IAtom) - Method in interface etomica.association.AssociationDefinition
isAssociated(IMolecule, IMolecule) - Method in interface etomica.association.AssociationDefinitionMolecule
isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolume
isAssociated(IMolecule, IMolecule) - Method in class etomica.association.BiasVolume2SiteAceticAcid: Function to check for bonding calculate the distance between atom1 and atom2
isAssociated(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeAceticAcid: Function to check for bonding calculate the distance between atom1 and atom2
isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeCube: Function to check for bonding
isAssociated(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeMolecule
isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphere: Function to check for bonding calculate the distance between atom1 and atom2
isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOriented: Function to check for bonding calculate the distance between atom1 and atom2
isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites: Function to check for bonding calculate the distance between atom1 and atom2
isAssociation - Variable in class etomica.models.OPLS.P2AceticAcidTwoSite
isAssociation - Variable in class etomica.models.water.P2HardAssociationGCPMReference
isAssociation - Variable in class etomica.models.water.PNWaterGCPMThreeSite
isAV(Object) - Static method in class org.jmol.util.Escape
isAxisSymmetric - Variable in class etomica.species.SpeciesSpheresRotating
isAxisSymmetric() - Method in class etomica.species.SpeciesSpheresRotating
isB - Variable in class etomica.virial.ClusterWheatleyExtendSW
isBeta - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
isBeta - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
isBeta - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
isBetaHCP - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
isBetaHCP - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
isBetaHCP - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
isBetaLatticeSum - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
isBetaPhase - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
isBetaPhase() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
isBi - Variable in class etomica.graph.model.comparators.ComparatorBiConnected
isBi - Variable in class etomica.graph.operations.ReeHoover
isBi - Variable in class etomica.graph.property.FFTDecomposition
isBiColor() - Method in enum org.jmol.constant.EnumStereoMode
IsBiconnected - Class in etomica.graph.property
IsBiconnected() - Constructor for class etomica.graph.property.IsBiconnected
isBigInteger() - Method in class etomica.veos.bigdecimal.BigSurd: True if the value is integer.
isBigInteger() - Method in class etomica.veos.bigdecimal.Rational: True if the value is integer.
isBonded() - Method in class etomica.nbr.CriterionBondedSimple
isBonded(IAtom, IAtom) - Method in class etomica.potential.P2HardBondedList: Returns true if the pair of atoms are on each others' bonded list; false otherwise.
isBonded(IAtomList) - Method in class etomica.potential.P2HardBondedList
isBoundaryWall() - Method in class etomica.nbr.CriterionPositionWall: Returns true if the walls are at the box boundaries.
isBroken - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
isCellEditable(int, int) - Method in class etomica.graphics.DeviceTableModelGeneric
isCellEditable(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
isCellEditable(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
isCellEditable(int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
isClipped(int, int) - Method in class org.jmol.util.GData
isClipped3(int, int, int) - Method in class org.jmol.util.GData
isClippedXY(int, int, int) - Method in class org.jmol.util.GData
isClippedZ(int) - Method in class org.jmol.util.GData
isCloseFileEachTime() - Method in class etomica.data.DataLogger
isCO2 - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
isColixColorInherited(short) - Static method in class org.jmol.util.Colix
isColixLastAvailable(short) - Static method in class org.jmol.util.Colix
isColixTranslucent(short) - Static method in class org.jmol.util.Colix
isCollapseOnReset() - Method in class etomica.util.HistoryComplete: Returns true if the history is collapsed (to 100 data points) when reset is called.
isColorSolid - Variable in class org.jmol.util.MeshSurface
isCompatible(Edge) - Method in interface etomica.graph.model.Edge
isCompatible(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
isCompatible(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
isCompatible(Node) - Method in class etomica.graph.model.impl.NodeImpl
isCompatible(Metadata) - Method in interface etomica.graph.model.Metadata
isCompatible(Node) - Method in interface etomica.graph.model.Node
isCon - Variable in class etomica.graph.operations.SplitGraph
isConnected - Variable in class etomica.graph.property.HasSimpleArticulationPoint
isConnected() - Method in class etomica.graph.property.HasSimpleArticulationPoint
IsConnected - Class in etomica.graph.property
IsConnected() - Constructor for class etomica.graph.property.IsConnected
isConnected(int) - Method in class etomica.virial.cluster.ClusterGenerator: Determines if the cluster is connected after removal of the given node.
isConnected() - Method in class etomica.virial.cluster.ClusterGenerator: Determines if the cluster is connected.
isDead() - Method in interface etomica.graph.isomorphism.SearchState
isDead() - Method in class etomica.graph.isomorphism.UllmanSearchState
isDead() - Method in class etomica.graph.isomorphism.VF2SearchState
isDead() - Method in class etomica.graph.isomorphism.VFSearchState
isDecimalMode() - Method in class etomica.util.ScientificFormat
isDecimalSeparatorAlwaysShown() - Method in class etomica.util.ScientificFormat
isDirectedTowardsCamera(short) - Method in class org.jmol.g3d.Graphics3D
isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
isDisplayAntialiased() - Method in class org.jmol.util.GData: is full scene / oversampling antialiasing GENERALLY in effect
isDoClear() - Method in class etomica.graphics.DisplayPlot
isDoLatticeSum - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
isDoLegend() - Method in class etomica.graphics.DisplayPlot: Accessor for flag determining if a legend is to be shown.
isDoPBC() - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
isDoPBC() - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
isDoScaling() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
isDoWiggle() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
isDynamic - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
isDynamic - Variable in class etomica.AlkaneEH.SpeciesMethane
isDynamic - Variable in class etomica.chem.models.Model
isDynamic - Variable in class etomica.models.nitrogen.SpeciesN2
isDynamic - Variable in class etomica.models.nitrogen.SpeciesN2B
isDynamic - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
isDynamic - Variable in class etomica.models.water.SpeciesWater3P
isDynamic - Variable in class etomica.models.water.SpeciesWater3POriented
isDynamic - Variable in class etomica.models.water.SpeciesWater4P
isDynamic - Variable in class etomica.models.water.SpeciesWater4PCOM
isDynamic - Variable in class etomica.models.water.SpeciesWater4POriented
isDynamic - Variable in class etomica.normalmode.SpeciesHSDimer
isDynamic - Variable in class etomica.paracetamol.SpeciesParacetamol
isDynamic - Variable in class etomica.species.SpeciesSpheres
isDynamic() - Method in class etomica.species.SpeciesSpheres
isDynamic - Variable in class etomica.species.SpeciesSpheresCustom
isDynamic() - Method in class etomica.species.SpeciesSpheresCustom
isDynamic - Variable in class etomica.species.SpeciesSpheresHetero
isDynamic() - Method in class etomica.species.SpeciesSpheresHetero
isDynamic - Variable in class etomica.species.SpeciesSpheresMono
isDynamic() - Method in class etomica.species.SpeciesSpheresMono
isDynamic - Variable in class etomica.virial.Species7SiteRigidSF6
isDynamic - Variable in class etomica.virial.SpeciesAlkaneEH
isDynamic - Variable in class etomica.virial.SpeciesAnthracene3site464
isDynamic - Variable in class etomica.virial.SpeciesAnthracene3site545
isDynamic - Variable in class etomica.virial.SpeciesMethane
isDynamic - Variable in class etomica.virial.SpeciesPh3site464
isDynamic - Variable in class etomica.virial.SpeciesPh3site545
isDynamic - Variable in class etomica.virial.SpeciesTraPPEAnthracene
isDynamic - Variable in class etomica.virial.SpeciesTraPPECO2
isDynamic - Variable in class etomica.virial.SpeciesTraPPENaphthalene
isDynamic - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
isEditable() - Method in class etomica.graphics.DeviceBox
isElementary() - Method in class etomica.virial.cluster.ClusterGenerator: Convenience method to determine whether the cluster is elementary or not.
isEmpty() - Method in class etomica.atom.AtomArrayList
isEmpty() - Method in class etomica.atom.MoleculeArrayList
isEmpty() - Method in class etomica.graph.model.GraphList
isEmpty(Graph) - Method in class etomica.graph.property.FactorFFT
isEmpty(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
isEmpty() - Method in class etomica.util.ObjectArrayList: Tests if this list has no elements.
isEmpty() - Method in class org.jmol.util.BitSet: Returns true if this BitSet contains no bits that are set to true.
isEnabled() - Method in interface etomica.api.IPotentialMaster
isEnabled(IPotentialMolecular) - Method in interface etomica.api.IPotentialMaster: Returns true if the potential is in this group and has not been disabled via a previous call to setEnabled; returns false otherwise.
isEnabled(IPotentialAtomic) - Method in interface etomica.api.IPotentialMaster: Returns true if the potential is in this group and has not been disabled via a previous call to setEnabled; returns false otherwise.
isEnabled() - Method in class etomica.graphics.DeviceSlider
isEnabled(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup: Returns true if the potential is in this group and has not been disabled via a previous call to setEnabled; returns false otherwise.
isEnabled() - Method in class etomica.potential.PotentialMaster
isEnabled(IPotentialAtomic) - Method in class etomica.potential.PotentialMaster
isEnabled(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
isEnabled() - Method in class etomica.potential.PotentialMasterLrc
isEnabled() - Method in class etomica.util.Grabber.ActionCornerSetter
isEnabled - Variable in class etomica.util.Grabber.DefaultMouseListener
isEnablePBC() - Method in class etomica.models.nitrogen.P2Nitrogen
isEqualTo(Quaternion) - Method in class etomica.math.Quaternion: Returns whether the Quaternion is equal to another given Quaternion p
isExpanded - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
isExponentialMode() - Method in class etomica.util.ScientificFormat
isFatal - Variable in exception etomica.graph.view.rasterizer.SVGConverterException: Defines whether or not this is a fatal error condition
isFatal() - Method in exception etomica.graph.view.rasterizer.SVGConverterException
isFeasiblePair(NodePair) - Method in interface etomica.graph.isomorphism.SearchState
isFeasiblePair(NodePair) - Method in class etomica.graph.isomorphism.UllmanSearchState
isFeasiblePair(NodePair) - Method in class etomica.graph.isomorphism.VF2SearchState
isFeasiblePair(NodePair) - Method in class etomica.graph.isomorphism.VFSearchState
IsFFT - Class in etomica.graph.property: Property class that determines if a diagram can be decomposed by FFT.
IsFFT() - Constructor for class etomica.graph.property.IsFFT
IsFFT - Class in etomica.virial
IsFFT() - Constructor for class etomica.virial.IsFFT
isFile(File) - Method in class etomica.graph.view.rasterizer.SVGConverter: Returns true if f is a File.
isFitToWindow() - Method in class etomica.graphics.DisplayTable: Accessor method for flag determining if table is squeezed to fit in window.
isFlexibleMode() - Method in class etomica.util.ScientificFormat
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
isGamma - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
isGamma - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
isGoal() - Method in interface etomica.graph.isomorphism.SearchState
isGoal() - Method in class etomica.graph.isomorphism.UllmanSearchState
isGoal() - Method in class etomica.graph.isomorphism.VF2SearchState
isGoal() - Method in class etomica.graph.isomorphism.VFSearchState
isGraphic - Variable in class etomica.AlkaneEH.CH4NVT.Param
isGraphic - Variable in class etomica.AlkaneEH.DHS_NVT.Param
isGraphic - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
isGraphic - Variable in class etomica.dielectric.DHS_NVT.Param
isGraphic - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
isGraphic - Variable in class etomica.dielectric.TIP4P_NVT.Param
isGraphics - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
isGroupingUsed() - Method in class etomica.util.ScientificFormat
isHeadless() - Method in interface org.jmol.api.ApiPlatform
isHeadless() - Method in class org.jmol.awt.Platform
isHetero(String) - Static method in class org.jmol.viewer.JmolConstants
isHOptimizer() - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
isIce - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
isIce - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
isIce - Variable in class etomica.models.water.ConfigurationFileTIP4P
isIgnoreOverlap() - Method in class etomica.action.IntegratorReset
isIgnoreOverlap() - Method in class etomica.action.SimulationRestart
isIgnoreOverlap() - Method in class etomica.zeolite.ZeoliteSimStart
isIllegal() - Method in class etomica.math.Quaternion: Returns true if even a single component of the quaternion is either infinite or NaN
ISimulation - Interface in etomica.api: The ISimulation is an interface for a simulation, containing boxes, species, a random number generator and an integrator.
ISimulationAtomTypeEvent - Interface in etomica.api
ISimulationAtomTypeIndexEvent - Interface in etomica.api
ISimulationBoxEvent - Interface in etomica.api
ISimulationEvent - Interface in etomica.api
ISimulationEventManager - Interface in etomica.api
ISimulationIndexEvent - Interface in etomica.api
ISimulationListener - Interface in etomica.api
ISimulationSpeciesEvent - Interface in etomica.api
ISimulationSpeciesIndexEvent - Interface in etomica.api
isIncludeAdiabatic() - Method in class etomica.graphics.DeviceThermoSelector
isIncludeLrc() - Method in class etomica.atom.iterator.IteratorDirective: Sets flag indicating if lrc potentials (long-range correction) should be included.
isIncludeLrc() - Method in class etomica.data.meter.MeterHyperVirial: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.data.meter.MeterPotentialEnergy: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.data.meter.MeterPressure: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.data.meter.MeterPressureMolecular: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.data.meter.MeterPressureTensor: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.liquidLJ.MeterPU: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.modules.vle.MeterPressure2: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.normalmode.MeterPressureSuperBox: Indicates whether calculated energy should include long-range correction for potential truncation (true) or not (false).
isIncludeLrc() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
isIncludeLrc() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
isIncludeLrc() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
isIncludeLrc() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
isInDisplayRange(int, int) - Method in class org.jmol.util.GData
isInteger() - Method in class etomica.graphics.DeviceBox
isInteger() - Method in class etomica.veos.bigdecimal.Rational: True if the value is integer and in the range of the standard integer.
isIntegerDisplay() - Method in class etomica.graphics.DisplayTextBox
isIntegerFrac() - Method in class etomica.veos.bigdecimal.Rational: True if the value is a fraction of two integers in the range of the standard integer.
isInteractingList - Variable in class etomica.nbr.list.AtomPotentialList
isInteractingList - Variable in class etomica.nbr.list.molecule.MoleculePotentialList
isInteractive - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
isInteractive - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
isInteractive - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
isInteractive - Variable in class etomica.virial.cluster.VirialDiagrams
isInteractive - Variable in class etomica.virial.cluster.VirialDiagramsMix
isInteractive - Variable in class etomica.virial.cluster.VirialDiagramsMix2
isInteractive - Variable in class etomica.virial.cluster.VirialDiagramsPT
isInteractive - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
isInteractive - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
isInTetrahedron(Point3f, Point3f, Point3f, Point3f, Point3f, Point4f, Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
isIntraMolecular() - Method in class etomica.nbr.CriterionMolecular: Flag indicating whether to accept intra- (if argument is true) or inter- (if argument is false) molecular pairs.
isIsoFree() - Method in class etomica.graph.engine.impl.ConstructorColoredImpl
isIsoFree() - Method in class etomica.graph.engine.impl.ConstructorMonoImpl
isIsoFree() - Method in interface etomica.graph.engine.Parser.ConstructorColored
isIsoFree() - Method in interface etomica.graph.engine.Parser.ConstructorMono
isIsomorphOf(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagram: Returns true if this cluster is an isomorph of the given cluster.
isIsothermal() - Method in class etomica.graphics.DeviceThermoSlider
isIsothermal() - Method in class etomica.integrator.IntegratorBox
isIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
iskiosk - Static variable in class org.jmol.script.Token
isLazySafe() - Method in interface g3dsys.control.IndexIterator: Indicates whether it is appropriate to simply scale the original boundary lines when in 'large box' mode.
isLiquid - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
isLJ - Variable in class etomica.normalmode.MeterSolidProps
isLS - Variable in class etomica.normalmode.PotentialCalculationEFSSP
isMatch(String, String, boolean, boolean) - Static method in class org.jmol.util.TextFormat
isMaximumScore() - Method in class etomica.virial.cluster.ClusterGenerator: Determines if the cluster has a maximum score.
isMerged - Variable in class org.jmol.util.MeshSurface
ISMORPHS_COUNT - Static variable in class etomica.graph.isomorphism.Match
isMovable() - Method in class etomica.graphics.DisplayCanvas
isMovable() - Method in class etomica.graphics.DisplayPolytope
isNaN() - Method in interface etomica.api.IVector: Returns true if any element of the vector is not-a-number.
isNaN() - Method in interface etomica.data.IData: Returns true if any data value is true for Double.isNaN
isNaN() - Method in class etomica.data.types.DataDouble: Returns true if the this instance's value is NaN.
isNaN() - Method in class etomica.data.types.DataDoubleArray: Returns true if any element of the encapsulated array is not-a-number, as given by Double.isNaN.
isNaN() - Method in class etomica.data.types.DataDoubleBDArray
isNaN() - Method in class etomica.data.types.DataGroup
isNaN() - Method in class etomica.data.types.DataTensor: Returns true if any vector element is not-a-number, as given by Double.isNaN.
isNaN() - Method in class etomica.data.types.DataVector: Returns true if any vector element is not-a-number, as given by Double.isNaN.
isNaN() - Method in interface etomica.space.Tensor
isNaN() - Method in class etomica.space1d.Tensor1D
isNaN() - Method in class etomica.space1d.Vector1D
isNaN() - Method in class etomica.space2d.Tensor2D
isNaN() - Method in class etomica.space2d.Vector2D
isNaN() - Method in class etomica.space3d.Tensor3D
isNaN() - Method in class etomica.space3d.Vector3D
isNaN() - Method in class etomica.spaceNd.TensorND
isNaN() - Method in class etomica.spaceNd.VectorND
isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
isNewPair - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
isNewPair - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
isNodalPoint(int) - Method in class etomica.virial.cluster.ClusterGenerator: Determines if the given node is a nodal point.
isNominallyPerParticleFrequency() - Method in class etomica.integrator.mcmove.MCMoveBox: Indicates whether this move should nominally be performed at a frequency proportional to the number of molecules in the box.
IsoFree - Class in etomica.graph.operations
IsoFree() - Constructor for class etomica.graph.operations.IsoFree
isoFree - Variable in class etomica.graph.operations.Split
IsoFree.IsoFreeParams - Class in etomica.graph.operations
IsoFreeParams() - Constructor for class etomica.graph.operations.IsoFree.IsoFreeParams
IsomorphismFilter - Class in etomica.graph.iterators.filters
IsomorphismFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.IsomorphismFilter
IsomorphismFilter(GraphIterator, GlobalFilter.SignatureMaker) - Constructor for class etomica.graph.iterators.filters.IsomorphismFilter
IsomorphismPrefilteredPartitionedIterator - Class in etomica.graph.iterators
IsomorphismPrefilteredPartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) - Constructor for class etomica.graph.iterators.IsomorphismPrefilteredPartitionedIterator
isOneEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
isOneEVal() - Method in class etomica.normalmode.IntegratorHarmonic
isOneOf(String, String) - Static method in class org.jmol.util.Parser
isOneWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
isOneWV() - Method in class etomica.normalmode.IntegratorHarmonic
isOnlyHardRod - Variable in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
isosurface - Static variable in class org.jmol.script.Token
isosurfacekey - Static variable in class org.jmol.script.Token
isosurfacepropertysmoothing - Static variable in class org.jmol.script.Token
isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.Token
isothermal - Variable in class etomica.integrator.IntegratorBox
ISpace - Interface in etomica.space
isPaletteVariable(byte) - Static method in enum org.jmol.constant.EnumPalette
isPass2 - Variable in class org.jmol.util.GData
isPass2() - Method in class org.jmol.util.GData
isPauseAfterEachAction() - Method in class etomica.action.activity.ActivityGroupSeries
isPaused() - Method in class etomica.action.activity.ActivityGroupSeries
isPaused() - Method in class etomica.action.Activity: Queries whether the integrator is in a state of being paused.
ISpecies - Interface in etomica.api: An ISpecies holds information about how to construct a molecule, and creates molecules on demand.
ISpeciesOriented - Interface in etomica.species
isPeriodic - Variable in class etomica.lattice.RectangularLatticeNbrIterator
isPositive() - Method in class etomica.veos.BigValue
isPositive() - Method in interface etomica.veos.IBigValue: Returns true if this instance has a value greater than zero.
isPositive() - Method in class etomica.veos.MyBigDecimal
isPositiveSide(IVector) - Method in class etomica.lattice.LatticePlane: Returns true if the given point is on the side of the plane toward which the normal vector points.
isPositiveSide(IVector) - Method in class etomica.math.geometry.Plane: Returns true if the given point is on the side of the plane or over the side of the plane by epsilon or less toward which the normal vector points.
isPotentialSite(String, IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
isPT2 - Static variable in class etomica.potential.P2O2Bartolomei
isPT2 - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
isPT2 - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
isPureQuaternion() - Method in class etomica.math.Quaternion: Returns whether the Quaternion is pure or not
isqrt(int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate floor(sqrt(n)).
isqrt(long) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate floor(sqrt(n)).
isqrt(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate floor(sqrt(n)).
isQuiet() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
isQuiet() - Method in class etomica.nbr.list.NeighborListManager
isRadical - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
isRadical(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: This function return true if the given atom is a radical (meaning that it has only one unreacted site).
isRational() - Method in class etomica.veos.bigdecimal.BigSurd: True if the value is rational.
isReadable() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
isReadable() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
isReadable() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource: Checks if source can be read
isReadable() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
isReference - Variable in class etomica.overlap.MeterOverlap
isRejectable - Variable in class etomica.normalmode.IntegratorHarmonic
isRejectable - Variable in class etomica.normalmode.MCMoveHarmonic
isRejectable() - Method in class etomica.normalmode.MCMoveHarmonic
isRemoveSpeciesAfterAlertFlag() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
isRepeatCurrentAction() - Method in class etomica.action.activity.Controller: Returns value of repeatCurrentAction flag.
isRescalingToFitVolume() - Method in class etomica.config.ConfigurationLattice: Returns the resizeLatticeToFitVolume flag.
isRescalingToFitVolume() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice: Returns the resizeLatticeToFitVolume flag.
isRescalingToFitVolume() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice: Returns the resizeLatticeToFitVolume flag.
isResidual() - Method in class etomica.data.meter.MeterWidomInsertion: Accessor for flag specifying if full or residual chemical potential is computed
isResizable() - Method in class etomica.graphics.DisplayCanvas
isResizable() - Method in class etomica.graphics.DisplayPolytope
isRootPoint(int) - Method in class etomica.virial.cluster.ClusterDiagram: returns true if the given point is a root point
isSameAs(String) - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
isSameAs(String) - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
isSameAs(String) - Method in interface etomica.graph.view.rasterizer.SVGConverterSource: Checks if same as source described by srcStr
isSameAs(String) - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
isSameColor(Edge) - Method in interface etomica.graph.model.Edge
isSameColor(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
isSameColor(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
isSameColor(Node) - Method in class etomica.graph.model.impl.NodeImpl
isSameColor(Metadata) - Method in interface etomica.graph.model.Metadata
isSameColor(Node) - Method in interface etomica.graph.model.Node
isSameFileEachTime() - Method in class etomica.data.DataLogger
isSameId(Edge) - Method in interface etomica.graph.model.Edge
isSameId(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
isSameId(Node) - Method in class etomica.graph.model.impl.NodeImpl
isSameId(Node) - Method in interface etomica.graph.model.Node
isSameType(Metadata) - Method in class etomica.graph.model.impl.EdgeImpl
isSameType(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
isSameType(Metadata) - Method in class etomica.graph.model.impl.NodeImpl
isSameType(Metadata) - Method in interface etomica.graph.model.Metadata
isSatisfied(FeatureSet) - Method in class etomica.compatibility.ClassRequirement
isSatisfied(FeatureSet) - Method in class etomica.compatibility.FeatureRequirement
isSatisfied(FeatureSet) - Method in class etomica.compatibility.Requirement
isSatisfied(FeatureSet) - Method in class etomica.compatibility.RequirementSet
isSelected(String) - Method in class etomica.graphics.DeviceButtonGroup: Returns true if the button of the given label is selected.
isSelectMode - Variable in class etomica.normalmode.MCMoveHarmonic
isShapeSecondary(int) - Static method in class org.jmol.viewer.JmolConstants
isShowBorder() - Method in class etomica.graphics.DeviceSlider
isShowBorder() - Method in class etomica.graphics.DeviceSpinner
isShowingColumnHeaders() - Method in class etomica.graphics.DisplayTable
isShowingRowLabels() - Method in class etomica.graphics.DisplayTable: Accessor method for flag indicating if table should include a column of "x" values.
isShowingUnits() - Method in class etomica.graphics.DisplayTable
isShowValues() - Method in class etomica.graphics.DeviceTernarySelector: Accessor method for flag indicating if values are shown in accompanying text boxes.
isSingleThreaded() - Method in interface org.jmol.api.ApiPlatform
isSingleThreaded() - Method in class org.jmol.awt.Platform
isSpecies1AtomicFlag() - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
isSpecies2AtomicFlag() - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
isSpeciesAlreadyAdded(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
isSpeciesSelectionChanged() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
isSPP(BigInteger, BigInteger) - Method in class etomica.veos.bigdecimal.Prime: Test whether a number n is a strong pseudoprime to base a.
issquare() - Method in class etomica.veos.bigdecimal.Ifactor: Test whether this is a square of an integer (perfect square).
isStationary() - Method in class etomica.potential.P1HardMovingBoundary
isStopSimulation() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
isStringArray(String) - Static method in class org.jmol.util.Escape
isThermalEllipsoid - Variable in class org.jmol.util.Quadric
isTransposed() - Method in class etomica.graphics.DisplayTable: If true, each data set fills a row; if false, data are arranged to fill columns.
isTrial - Variable in class etomica.virial.BoxCluster
isTriangleSet - Variable in class org.jmol.util.MeshSurface
iSubstep - Variable in class etomica.thermointegration.IntegratorThermodynamic
isUnitQuaternion() - Method in class etomica.math.Quaternion: Returns whether the norm of the Quaternion is 1 or not
isUpdatingOnAnyChange() - Method in class etomica.data.DataSet
isUpperBound - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
iSurf - Variable in class etomica.potential.P2WaterPotentialsJankowski
iSurf - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
isUsePermutations() - Method in class etomica.virial.ClusterBonds: Returns the usePermutations flag.
isValid(double[][][]) - Method in interface etomica.virial.ClusterSumAssociation.ClusterCriteria
isVariableType(Object) - Static method in class org.jmol.script.ScriptVariable
isVolFluctuation() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
isWild(String) - Static method in class org.jmol.util.TextFormat
isWithin(Point3f) - Method in class org.jmol.util.BoxInfo
isWriteable(File) - Method in class etomica.graph.view.rasterizer.SVGConverter: Checks if the application is allowed to write to the file.
isWriteOnInterval() - Method in class etomica.data.DataLogger
isXComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
isXFlipped() - Method in class g3dsys.control.G3DSys
isYComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
isYFlipped() - Method in class g3dsys.control.G3DSys
isyst - Static variable in class etomica.potential.P2WaterPotentialsJankowski
isZero() - Method in interface etomica.api.IVector: Returns true if all components of this vector are zero; false otherwise.
isZero() - Method in class etomica.space1d.Vector1D
isZero() - Method in class etomica.space2d.Vector2D
isZero() - Method in class etomica.space3d.Vector3D
isZero() - Method in class etomica.spaceNd.VectorND
isZero() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Test whether this polynomial value is zero.
isZero() - Method in class etomica.veos.BigValue
isZero() - Method in interface etomica.veos.IBigValue: Returns true if this instance has a value of zero.
isZero() - Method in class etomica.veos.MyBigDecimal
iT - Variable in class etomica.potential.PotentialCalculationPhiSum
iTag - Variable in class etomica.normalmode.MeterTiltRotationHistogram
iTemperatureStep - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
itemsInList - Variable in class etomica.atom.AtomArrayList
itemsInList - Variable in class etomica.atom.MoleculeArrayList
itemStateChanged(ItemEvent) - Method in class etomica.graphics.DimensionedDoubleEditor: ItemListener interface implementation.
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.BondInteractionTypeToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.BondTypeToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ConnectedToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.GraphicsToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.NumbersToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.PointsToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
itemStateChanged(ItemEvent) - Method in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
iterate - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
iterate - Variable in class etomica.util.numerical.NonLinearCurveFitting
iterator - Variable in class etomica.data.meter.MeterDihedralAngle
iterator - Variable in class etomica.data.meter.MeterRDF
iterator - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
iterator() - Method in class etomica.graph.model.GraphList
Iterator(int) - Constructor for class etomica.lattice.RectangularLattice.Iterator
iterator - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
iterator - Variable in class etomica.normalmode.MCMoveHarmonic
iterator - Variable in class etomica.normalmode.MCMoveHarmonicStep
iterator - Variable in class etomica.potential.PotentialGroup.PotentialLinker
iterator - Variable in class etomica.potential.PotentialMaster.PotentialLinker
IteratorDirective - Class in etomica.atom.iterator: Encapsulation of a set of instructions that an AtomsetIterator uses to select the atoms it presents on iteration.
IteratorDirective() - Constructor for class etomica.atom.iterator.IteratorDirective
IteratorDirective(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.IteratorDirective
IteratorDirective(IteratorDirective.Direction, IAtom) - Constructor for class etomica.atom.iterator.IteratorDirective
IteratorDirective(IteratorDirective.Direction, IMolecule) - Constructor for class etomica.atom.iterator.IteratorDirective
iteratorDirective - Variable in class etomica.data.meter.MeterHyperVirial
iteratorDirective - Variable in class etomica.data.meter.MeterPotentialEnergy
iteratorDirective - Variable in class etomica.data.meter.MeterPressureTensor
iteratorDirective - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
iteratorDirective - Variable in class etomica.liquidLJ.MeterPU
iteratorDirective - Variable in class etomica.liquidLJ.MeterPUCut
iteratorDirective - Variable in class etomica.liquidLJ.MeterPUCutLS
IteratorDirective.Direction - Class in etomica.atom.iterator
IteratorDirective.PotentialCriterion - Class in etomica.atom.iterator: Class used to define a criterion that must be satisfied by a potential in order for its atoms to be approved for iteration by an iterator directive.
IteratorEF(byte, boolean) - Constructor for class etomica.virial.PYGenerator.IteratorEF
IteratorFactory - Class in etomica.atom.iterator: Class for construction of iterators of molecules.
IteratorFactory() - Constructor for class etomica.atom.iterator.IteratorFactory
iteratorFactory - Variable in class etomica.potential.PotentialMaster
IteratorToSet - Class in etomica.graph.iterators
IteratorToSet() - Constructor for class etomica.graph.iterators.IteratorToSet
IteratorWrapper - Class in etomica.graph.iterators
IteratorWrapper(Iterator<Graph>) - Constructor for class etomica.graph.iterators.IteratorWrapper
IteratorWrapper(Iterator<Graph>, boolean) - Constructor for class etomica.graph.iterators.IteratorWrapper
iThread - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
iThread - Variable in class etomica.virial.MeterVirialBinMultiThreaded
iThread - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
iThread - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
iThread - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
itypus - Static variable in class etomica.potential.P2WaterPotentialsJankowski
iValue(Token) - Static method in class org.jmol.script.ScriptVariable
IVector - Interface in etomica.api: Basic vector interface containing methods needed for basic vector operations and other accessor methods.
IVectorMutable - Interface in etomica.api: Vector interface containing methods needed for vector operations which alter the contents of the vector.
IVectorRandom - Interface in etomica.space: Vector interface for vectors having random number methods
iweight - Static variable in class etomica.potential.P2WaterPotentialsJankowski
iy - Variable in class etomica.util.numerical.AkimaSplineSmootherDy

J

jLabel - Variable in class etomica.graphics.DisplayTextBox: Descriptive text label to be displayed with the value
jmax - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
jmol - Static variable in class org.jmol.script.Token
JmolConstants - Class in org.jmol.viewer
JmolConstants() - Constructor for class org.jmol.viewer.JmolConstants
JmolFont - Class in org.jmol.util: Provides font support using a byte fid (Font ID) as an index into font table.
jNew - Variable in class etomica.normalmode.MCMovePhaseAngle
jNew - Variable in class etomica.normalmode.MCMoveWV
join(String[], char, int) - Static method in class org.jmol.util.TextFormat
jOld - Variable in class etomica.normalmode.MCMovePhaseAngle
jOld - Variable in class etomica.normalmode.MCMoveWV
Joule - Class in etomica.units: The Joule unit of energy, equal to 1 N-m or 1 kg-m^2/s^2.
JouleThomson - Class in etomica.modules.joulethomson: Joule Thomson Experiment Ed Maginn [University of Notre Dame], David Kofke [University at Buffalo] Permits study of a system undergoing isothermal or isenthalpic expansion and compression.
JouleThomson(JouleThomsonSim, Space) - Constructor for class etomica.modules.joulethomson.JouleThomson
JouleThomson.Applet - Class in etomica.modules.joulethomson
JouleThomson.SpeciesChooser - Class in etomica.modules.joulethomson
JouleThomsonSim - Class in etomica.modules.joulethomson
JouleThomsonSim() - Constructor for class etomica.modules.joulethomson.JouleThomsonSim
JouleThomsonSim(Space) - Constructor for class etomica.modules.joulethomson.JouleThomsonSim
JPEG - Static variable in class etomica.graph.view.rasterizer.DestinationType
JPEG_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
JPEG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
JPEG_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
JPerHartree - Static variable in class etomica.potential.P2QChemInterpolated
JPerHartree - Static variable in class etomica.virial.B3ForSphericallySymmetricU
jsonOutputFileName - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
jsonOutputFileName - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
jsonOutputFileName - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
jsonOutputFileName - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
jsonOutputFileName - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
jsonOutputFileName - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
jumpCount - Variable in class etomica.lattice.RectangularLattice
justDADB - Static variable in class etomica.normalmode.MeterDADB
justifymeasurements - Static variable in class org.jmol.script.Token
justU - Static variable in class etomica.normalmode.MeterDADB

K

k - Static variable in class etomica.potential.P2QChemInterpolated
K - Variable in class etomica.util.numerical.VirialOptimizer.VirialParam
k - Static variable in class etomica.virial.B3ForSphericallySymmetricU
kbeta(int) - Method in interface etomica.veos.BetaSource: Returns k * beta(k), which in some cases has better precision than beta(k) itself.
kbeta(int) - Method in class etomica.veos.HardRods
kbeta(int) - Method in class etomica.veos.VanderWaals
kBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
kBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
kBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kc - Variable in class etomica.dimer.P1LepsHarmonic
kCut - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
kCut - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
kCut - Variable in class etomica.potential.EwaldSummation
kDistributionHash - Variable in class etomica.virial.CalcFFT
Kelvin - Class in etomica.units
KEMax - Variable in class etomica.graphics.ColorSchemeTemperature
KEMin - Variable in class etomica.graphics.ColorSchemeTemperature
kEpsilon - Variable in class etomica.models.co2.PNGCPMX
keyPressed(KeyEvent) - Method in class etomica.graphics.PropertyText
keyReleased(KeyEvent) - Method in class etomica.graphics.PropertyText
keySelect(char) - Static method in class etomica.units.Prefix: Returns a prefix corresponding to the given key.
keyTyped(KeyEvent) - Method in class etomica.graphics.PropertyText
kFactory - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
kg1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
kg1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
kg1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg1BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
kg1BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
kg1BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
kg2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg2BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
kg2BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg3BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kg4BondMinus - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
kGamma - Variable in class etomica.models.co2.PNGCPMX
kijEpsilon - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
kijGamma - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
kijSigma - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
KILO - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺³ = 1000.
kinetic - Variable in class etomica.data.meter.MeterEnergy
kIntra0 - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
kSigma - Variable in class etomica.models.co2.PNGCPMX
kStart - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
kVector - Variable in class etomica.potential.EwaldSummation

L

L - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
L - Variable in class etomica.normalmode.ConformationHSDimer
L - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
L - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
L - Static variable in class etomica.potential.P3HydrogenManzhos
L - Variable in class etomica.util.numerical.VirialOptimizer.VirialParam
label - Variable in class etomica.data.DataInfoFactory
label - Variable in class etomica.graphics.DeviceBox: Descriptive text label to be displayed with the value
label - Variable in class etomica.graphics.Display
label - Static variable in class org.jmol.script.Token
LABEL_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
LABEL_DEFAULT_X_OFFSET - Static variable in class org.jmol.viewer.JmolConstants
LABEL_DEFAULT_Y_OFFSET - Static variable in class org.jmol.viewer.JmolConstants
LABEL_MAXIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
LABEL_MINIMUM_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
labelHash - Variable in class etomica.graphics.DeviceButtonGroup
labelList - Variable in class etomica.graphics.DisplayPlot
labelPosition - Variable in class etomica.graphics.DisplayTextBoxesCAE
labels - Variable in class etomica.virial.cluster.ExchangeSplit
labelString - Variable in class etomica.graphics.DeviceBox
LabelType(String) - Constructor for class etomica.graphics.DeviceBox.LabelType
LabelType(String) - Constructor for class etomica.graphics.DisplayTextBox.LabelType
labelType - Variable in class etomica.graphics.DisplayTextBoxesCAE
labSums - Variable in class etomica.data.AccumulatorAverageCollapsingLogAB
lambda - Variable in class etomica.modules.adsorption.EOSSW
lambda - Variable in class etomica.modules.catalysis.P2SquareWellBonding
lambda - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
lambda - Variable in class etomica.modules.catalysis.P2SquareWellSurface
lambda - Variable in class etomica.modules.insertion.InsertionGraphic
lambda - Variable in class etomica.modules.mu.P2SquareWellOneSide
lambda - Variable in class etomica.modules.pistoncylinder.PistonCylinder
lambda - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
lambda - Variable in class etomica.modules.render.RenderMD.RenderMDParam
lambda - Variable in class etomica.modules.swmd.SwmdGraphic
lambda - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
lambda - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
lambda - Variable in class etomica.potential.P2DoubleWell
lambda - Variable in class etomica.potential.P2SquareWell
lambda - Variable in class etomica.potential.P2SquareWellRobust
lambda - Variable in class etomica.potential.P3HydrogenManzhos
lambda - Variable in class etomica.virial.P1IntraLambda
lambda - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
lambda - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
lambda - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
lambda - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
lambda - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
lambda - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
lambdas - Variable in class etomica.dimer.SimDimerLJadatom
lambdas - Variable in class etomica.dimer.SimDimerMEAMadatom
lambdas - Variable in class etomica.dimer.SimDimerMEAMGB
lambdas - Variable in class etomica.kmc.SimKMCMEAMadatom
lambdaSquared - Variable in class etomica.potential.P2PenetrableSquareWell
lambdaWF - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
lambdaWF - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
lamBox - Variable in class etomica.modules.insertion.InsertionGraphic
lamBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
lamBox - Variable in class etomica.modules.swmd.SwmdGraphic
lammpsFile - Variable in class etomica.interfacial.LJMC.LjMC3DParams
lammpsFile - Variable in class etomica.interfacial.LJMD.LJMDParams
language - Variable in class etomica.graph.view.rasterizer.SVGConverter: Language
language - Static variable in class org.jmol.script.Token
languagetranslation - Static variable in class org.jmol.script.Token
last - Static variable in class org.jmol.script.Token
LAST_AVAILABLE_COLIX - Static variable in class org.jmol.util.Colix
lastA - Variable in class etomica.normalmode.WriteS
lastAdjust - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
lastBoxIndex - Variable in class etomica.virial.PotentialCommonAtomic
lastBoxIndex - Variable in class etomica.virial.PotentialGroup3PI
lastBoxIndex - Variable in class etomica.virial.PotentialGroupPI
lastCollisionVirial() - Method in class etomica.modules.adsorption.P1Wall
lastCollisionVirial - Variable in class etomica.modules.catalysis.P2SquareWellBonding
lastCollisionVirial() - Method in class etomica.modules.catalysis.P2SquareWellBonding
lastCollisionVirial - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
lastCollisionVirial() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
lastCollisionVirial - Variable in class etomica.modules.catalysis.P2SquareWellSurface
lastCollisionVirial() - Method in class etomica.modules.catalysis.P2SquareWellSurface
lastCollisionVirial() - Method in class etomica.modules.colloid.P1Wall
lastCollisionVirial() - Method in class etomica.modules.mu.P1MagicWall: not yet implemented
lastCollisionVirial - Variable in class etomica.modules.mu.P2SquareWellOneSide
lastCollisionVirial() - Method in class etomica.modules.mu.P2SquareWellOneSide
lastCollisionVirial() - Method in class etomica.modules.osmosis.P1HardWall: not yet implemented
lastCollisionVirial() - Method in class etomica.normalmode.P2XOrder
lastCollisionVirial() - Method in class etomica.potential.P1HardBoundary
lastCollisionVirial() - Method in class etomica.potential.P1HardMovingBoundary
lastCollisionVirial() - Method in class etomica.potential.P1HardPeriodic: Returns zero.
lastCollisionVirial - Variable in class etomica.potential.P2DoubleWell
lastCollisionVirial() - Method in class etomica.potential.P2DoubleWell
lastCollisionVirial() - Method in class etomica.potential.P2HardAssociation
lastCollisionVirial() - Method in class etomica.potential.P2HardBond
lastCollisionVirial() - Method in class etomica.potential.P2HardBondedList
lastCollisionVirial - Variable in class etomica.potential.P2HardSphere
lastCollisionVirial() - Method in class etomica.potential.P2HardSphere
lastCollisionVirial() - Method in class etomica.potential.P2HardWrapper
lastCollisionVirial() - Method in class etomica.potential.P2Ideal: Returns zero.
lastCollisionVirial() - Method in class etomica.potential.P2PenetrableBond
lastCollisionVirial - Variable in class etomica.potential.P2PenetrableSphere
lastCollisionVirial() - Method in class etomica.potential.P2PenetrableSphere
lastCollisionVirial - Variable in class etomica.potential.P2PenetrableSquareWell
lastCollisionVirial() - Method in class etomica.potential.P2PenetrableSquareWell
lastCollisionVirial() - Method in class etomica.potential.P2RoughSphere
lastCollisionVirial - Variable in class etomica.potential.P2SquareWell
lastCollisionVirial() - Method in class etomica.potential.P2SquareWell
lastCollisionVirial - Variable in class etomica.potential.P2SquareWellRobust
lastCollisionVirial() - Method in class etomica.potential.P2SquareWellRobust
lastCollisionVirial() - Method in class etomica.potential.P2Tether
lastCollisionVirial() - Method in interface etomica.potential.PotentialHard: Value of the virial from the most recent collision.
lastCollisionVirialr2 - Variable in class etomica.modules.catalysis.P2SquareWellBonding
lastCollisionVirialr2 - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
lastCollisionVirialr2 - Variable in class etomica.modules.catalysis.P2SquareWellSurface
lastCollisionVirialr2 - Variable in class etomica.modules.mu.P2SquareWellOneSide
lastCollisionVirialr2 - Variable in class etomica.potential.P2DoubleWell
lastCollisionVirialr2 - Variable in class etomica.potential.P2HardSphere
lastCollisionVirialr2 - Variable in class etomica.potential.P2PenetrableSphere
lastCollisionVirialr2 - Variable in class etomica.potential.P2PenetrableSquareWell
lastCollisionVirialr2 - Variable in class etomica.potential.P2SquareWell
lastCollisionVirialr2 - Variable in class etomica.potential.P2SquareWellRobust
lastCollisionVirialTensor() - Method in class etomica.modules.adsorption.P1Wall
lastCollisionVirialTensor - Variable in class etomica.modules.catalysis.P2SquareWellBonding
lastCollisionVirialTensor() - Method in class etomica.modules.catalysis.P2SquareWellBonding
lastCollisionVirialTensor - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
lastCollisionVirialTensor() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
lastCollisionVirialTensor - Variable in class etomica.modules.catalysis.P2SquareWellSurface
lastCollisionVirialTensor() - Method in class etomica.modules.catalysis.P2SquareWellSurface
lastCollisionVirialTensor() - Method in class etomica.modules.colloid.P1Wall
lastCollisionVirialTensor() - Method in class etomica.modules.mu.P1MagicWall: not yet implemented.
lastCollisionVirialTensor - Variable in class etomica.modules.mu.P2SquareWellOneSide
lastCollisionVirialTensor() - Method in class etomica.modules.mu.P2SquareWellOneSide
lastCollisionVirialTensor() - Method in class etomica.modules.osmosis.P1HardWall: not yet implemented.
lastCollisionVirialTensor() - Method in class etomica.normalmode.P2XOrder
lastCollisionVirialTensor() - Method in class etomica.potential.P1HardBoundary
lastCollisionVirialTensor() - Method in class etomica.potential.P1HardMovingBoundary: not yet implemented.
lastCollisionVirialTensor() - Method in class etomica.potential.P1HardPeriodic: Returns null.
lastCollisionVirialTensor - Variable in class etomica.potential.P2DoubleWell
lastCollisionVirialTensor() - Method in class etomica.potential.P2DoubleWell
lastCollisionVirialTensor() - Method in class etomica.potential.P2HardAssociation
lastCollisionVirialTensor() - Method in class etomica.potential.P2HardBond
lastCollisionVirialTensor() - Method in class etomica.potential.P2HardBondedList
lastCollisionVirialTensor - Variable in class etomica.potential.P2HardSphere
lastCollisionVirialTensor() - Method in class etomica.potential.P2HardSphere
lastCollisionVirialTensor() - Method in class etomica.potential.P2HardWrapper
lastCollisionVirialTensor() - Method in class etomica.potential.P2Ideal: Returns a tensor of zeros.
lastCollisionVirialTensor() - Method in class etomica.potential.P2PenetrableBond
lastCollisionVirialTensor - Variable in class etomica.potential.P2PenetrableSphere
lastCollisionVirialTensor() - Method in class etomica.potential.P2PenetrableSphere
lastCollisionVirialTensor - Variable in class etomica.potential.P2PenetrableSquareWell
lastCollisionVirialTensor() - Method in class etomica.potential.P2PenetrableSquareWell
lastCollisionVirialTensor() - Method in class etomica.potential.P2RoughSphere
lastCollisionVirialTensor - Variable in class etomica.potential.P2SquareWell
lastCollisionVirialTensor() - Method in class etomica.potential.P2SquareWell
lastCollisionVirialTensor - Variable in class etomica.potential.P2SquareWellRobust
lastCollisionVirialTensor() - Method in class etomica.potential.P2SquareWellRobust
lastCollisionVirialTensor() - Method in class etomica.potential.P2Tether
lastCollisionVirialTensor() - Method in interface etomica.potential.PotentialHard: Value of the virial from the most recent collision, decomposed into it tensoral elements.
lastCPairID - Variable in class etomica.virial.ClusterChainHS
lastCPairID - Variable in class etomica.virial.ClusterChainSoft
lastCPairID - Variable in class etomica.virial.ClusterCoupledFlipped
lastCPairID - Variable in class etomica.virial.ClusterCoupledFlippedPartial
lastCPairID - Variable in class etomica.virial.ClusterSinglyConnected
lastCPairID - Variable in class etomica.virial.ClusterSum
lastCPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
lastCPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
lastCPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
lastCPairID - Variable in class etomica.virial.ClusterWheatleyHS
lastCPairID - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
lastCPairID - Variable in class etomica.virial.ClusterWheatleySoft
lastCPairID - Variable in class etomica.virial.ClusterWheatleySoftBD
lastCPairID - Variable in class etomica.virial.PotentialEmulCached
lastData - Variable in class etomica.data.DataPumpListenerPow
lastData - Variable in class etomica.data.DataPumpListenerSmart
lastDefaultdADef - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
lastDeltaU - Variable in class etomica.modules.mu.P1MagicWall
lastDMu - Variable in class etomica.normalmode.DataSourceMuRoot
lastDP - Variable in class etomica.normalmode.DataSourceMuRoot
lastDP - Variable in class etomica.normalmode.DataSourceMuRootPMatch
lastEnergies - Variable in class etomica.virial.PotentialEmulCached
lastEnergy - Variable in class etomica.normalmode.IntegratorHarmonic
lastEnergy - Variable in class etomica.normalmode.MCMoveHarmonic
lastEnergyChange - Variable in class etomica.modules.adsorption.P1Wall
lastEnergyChange - Variable in class etomica.modules.catalysis.P2SquareWellBonding
lastEnergyChange - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
lastEnergyChange - Variable in class etomica.modules.catalysis.P2SquareWellSurface
lastEnergyChange - Variable in class etomica.modules.colloid.P1Wall
lastEnergyChange - Variable in class etomica.modules.mu.P2SquareWellOneSide
lastEnergyChange - Variable in class etomica.potential.P2DoubleWell
lastEnergyChange - Variable in class etomica.potential.P2PenetrableSphere
lastEnergyChange - Variable in class etomica.potential.P2PenetrableSquareWell
lastEnergyChange - Variable in class etomica.potential.P2SquareWell
lastEnergyChange - Variable in class etomica.potential.P2SquareWellRobust
lastIndexOf(Object) - Method in class etomica.util.ObjectArrayList: Returns the index of the last occurrence of the specified Object in this list.
lastIndexOf(String) - Method in class org.jmol.util.StringXBuilder
lastLnTot - Variable in class etomica.normalmode.DataSourceMuRoot
lastLnTot - Variable in class etomica.normalmode.DataSourceMuRootPMatch
lastLPX - Static variable in class etomica.math.SpecialFunctions
lastMoveInsert() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
lastP - Variable in class etomica.normalmode.DataSourceMuRoot
lastP - Variable in class etomica.normalmode.DataSourceMuRoot1
lastP - Variable in class etomica.normalmode.DataSourceMuRootPMatch
lastPairID - Variable in class etomica.virial.PotentialCommonAtomic
lastPairID - Variable in class etomica.virial.PotentialGroup3PI
lastPairID - Variable in class etomica.virial.PotentialGroupPI
lastProfileTime - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
lastResult - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
lastStep - Variable in class etomica.liquidLJ.LjMd3D.ValueCache
lastStep - Variable in class etomica.liquidLJ.ValueCache
lastStepCount - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
lastStepCount - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
lastStepCount - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
lastStepPop - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
lastSubClusterValues - Variable in class etomica.virial.ClusterSumIC
lastThread - Variable in class etomica.action.activity.ActivityGroupParallel
lastTime - Variable in class etomica.data.DataSourceTensorVirialHard
lastTime - Variable in class etomica.data.meter.MeterPressureHard
lastTime - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
lastTime - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
lastTime - Variable in class etomica.modules.mu.DataSourceWallPressureMu
lastTime2 - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
lastU - Variable in class etomica.normalmode.MCMoveHarmonicEin
lastVacancyConcentration - Variable in class etomica.normalmode.DataSourceMuRoot
lastVacancyConcentration - Variable in class etomica.normalmode.DataSourceMuRoot1
lastVacancyConcentration - Variable in class etomica.normalmode.DataSourceMuRootPMatch
lastValue - Variable in class etomica.liquidLJ.LjMd3D.ValueCache
lastValue - Variable in class etomica.liquidLJ.ValueCache
lastValue - Variable in class etomica.virial.ClusterChainHS
lastValue - Variable in class etomica.virial.ClusterChainSoft
lastValue - Variable in class etomica.virial.ClusterCoupledFlipped
lastValue - Variable in class etomica.virial.ClusterCoupledFlippedPartial
lastValue - Variable in class etomica.virial.ClusterSinglyConnected
lastValue - Variable in class etomica.virial.ClusterSum
lastValue - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
lastValue - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
lastValue - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
lastValue - Variable in class etomica.virial.ClusterWheatleyHS
lastValue - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
lastValue - Variable in class etomica.virial.ClusterWheatleySoft
lastValue - Variable in class etomica.virial.ClusterWheatleySoftBD
lastValue - Variable in class etomica.virial.MayerFunctionThreeBody
lastVirial - Variable in class etomica.modules.adsorption.P1Wall
lastVirial - Variable in class etomica.modules.colloid.P1Wall
lastVirialTensor - Variable in class etomica.modules.adsorption.P1Wall
lastVirialTensor - Variable in class etomica.modules.colloid.P1Wall
lastWallVirial() - Method in class etomica.modules.adsorption.P1Wall
lastWallVirial() - Method in class etomica.modules.colloid.P1Wall
lastWallVirial() - Method in class etomica.potential.P1HardBoundary
lastWallVirial() - Method in class etomica.potential.P1HardMovingBoundary
lattice - Variable in class etomica.config.ConfigurationLattice
lattice - Variable in class etomica.config.ConfigurationLatticeSimple
lattice - Variable in class etomica.data.meter.MeterStructureFactor
lattice - Variable in class etomica.lattice.RectangularLatticeNbrIterator
lattice - Variable in class etomica.models.hexane.SimHarmonicHexane
lattice - Variable in class etomica.models.hexane.TestHexane
lattice - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
lattice - Variable in class etomica.models.hexane.TestHexaneFileConfig
lattice - Variable in class etomica.models.hexane.TestHexaneHarmonic
lattice - Variable in class etomica.models.hexane.TestSetToUHexane
lattice - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
lattice - Variable in class etomica.nbr.cell.NeighborCellManager
lattice - Variable in class etomica.normalmode.CoordinateDefinition
lattice - Variable in class etomica.normalmode.SimTarget
lattice - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
lattice - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
lattice - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
lattice - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
lattice - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
lattice - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
lattice - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
lattice - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
Lattice2ndDerivative(CoordinateDefinitionParacetamol, NumericalDerivativeEnergyParacetamol) - Constructor for class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
latticeBox - Variable in class etomica.normalmode.HSDimerNPT
latticeBox - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
latticeBox - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
latticeCorrec - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
LatticeCubicBcc - Class in etomica.lattice: Cubic primitive with a 2-site bcc basis.
LatticeCubicBcc(ISpace) - Constructor for class etomica.lattice.LatticeCubicBcc: Cubic bcc crystal with a lattice constant that gives a maximum-density structure for spheres of unit size.
LatticeCubicBcc(ISpace, double) - Constructor for class etomica.lattice.LatticeCubicBcc
LatticeCubicDiamond - Class in etomica.lattice: Cubic primitive with a 4-site fcc basis, on which each site is a 2-site diamond basis.
LatticeCubicDiamond(ISpace) - Constructor for class etomica.lattice.LatticeCubicDiamond: Cubic bcc crystal with a lattice constant that gives a maximum-density structure for spheres of unit size.
LatticeCubicDiamond(ISpace, double) - Constructor for class etomica.lattice.LatticeCubicDiamond
LatticeCubicFcc - Class in etomica.lattice: Cubic primitive with a 4-site fcc basis.
LatticeCubicFcc(ISpace) - Constructor for class etomica.lattice.LatticeCubicFcc: Cubic fcc crystal with a lattice constant that gives a maximum-density structure for spheres of unit size.
LatticeCubicFcc(ISpace, double) - Constructor for class etomica.lattice.LatticeCubicFcc
LatticeCubicSimple - Class in etomica.lattice: A simple cubic lattice, with one site per cubic unit cell.
LatticeCubicSimple(ISpace) - Constructor for class etomica.lattice.LatticeCubicSimple: Simple 3D cubic lattice with a unit lattice constant.
LatticeCubicSimple(ISpace, double) - Constructor for class etomica.lattice.LatticeCubicSimple: Makes a simple cubic lattice of a spatial dimension given by the first argument, and with the given lattice constant.
latticeDensity - Variable in class etomica.normalmode.DataSourceAvgPressure2
latticeDensity - Variable in class etomica.normalmode.DataSourceMuRoot
latticeDensity - Variable in class etomica.normalmode.DataSourceMuRoot1
latticeDensity - Variable in class etomica.normalmode.DataSourceMuRootPMatch
latticeDensity - Variable in class etomica.normalmode.DataSourcePMu
latticeEditor - Variable in class etomica.modules.crystalviewer.CrystalViewer
LatticeEditor - Class in etomica.modules.crystalviewer: Class that produces a panel with controls that permit editing of the structure of a lattice.
LatticeEditor(CrystalViewer, BravaisLattice[], String[], ISpace) - Constructor for class etomica.modules.crystalviewer.LatticeEditor
LatticeEditor.NModifier - Class in etomica.modules.crystalviewer
latticeEnergy - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
latticeEnergy - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
latticeEnergy - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
latticeEnergy - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
latticeEnergy - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
latticeEnergy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
latticeEnergy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
latticeEnergy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
latticeEnergy - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
latticeEnergy - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
latticeEnergy - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
latticeEnergy - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
latticeEnergy - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
latticeEnergy - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
latticeEnergy - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
latticeEnergy - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
latticeEnergy - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
latticeEnergy - Variable in class etomica.normalmode.HessianDB
latticeEnergy - Variable in class etomica.normalmode.HTTPSoftSphereSim
latticeEnergy - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
latticeEnergy - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
latticeEnergy - Variable in class etomica.normalmode.MCMoveHarmonicStep
latticeEnergy - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
latticeEnergy - Variable in class etomica.normalmode.MeterBoltzmannHTTP
latticeEnergy - Variable in class etomica.normalmode.MeterBoltzmannTarget
latticeEnergy - Variable in class etomica.normalmode.MeterDADB
latticeEnergy - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
latticeEnergy - Variable in class etomica.normalmode.MeterDirectSamplingTarget
latticeEnergy - Variable in class etomica.normalmode.MeterOverlapSwitch
latticeEnergy - Variable in class etomica.normalmode.MeterSolidDA
latticeEnergy - Variable in class etomica.normalmode.MeterSolidDACut
latticeEnergy - Variable in class etomica.normalmode.MeterTargetTP
latticeEnergy - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
latticeEnergy - Variable in class etomica.normalmode.MeterWorkBennetTarget
latticeEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
latticeEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
latticeEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
latticeEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
latticeEnergy - Variable in class etomica.normalmode.MeterWorkTargetBennet
latticeEnergy - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
latticeEnergy - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
latticeEnergy - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
latticeEnergy - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
latticeEnergy - Variable in class etomica.normalmode.SimBennet
latticeEnergy - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
latticeEnergy - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
latticeEnergy - Variable in class etomica.normalmode.SimHarmonicUmbrella
latticeEnergy - Variable in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphere
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
latticeEnergy - Variable in class etomica.normalmode.SimOverlapSSnxy
latticeEnergy - Variable in class etomica.normalmode.SimTargetUmbrella
latticeEnergy - Variable in class etomica.normalmode.SimUmbrella
latticeEnergy - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
LatticeEnergy(P2DLPOLY, CoordinateDefinitionParacetamol) - Constructor for class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
latticeEnergyDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
LatticeEnergyParacetamol - Interface in etomica.paracetamol
latticeEnergyRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
latticeEnergyTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
LATTICEHARMONIC - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
LATTICEHARMONIC - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
LatticeHcp - Class in etomica.lattice: Hexagonal primitive with a 2-site hcp basis.
LatticeHcp(ISpace) - Constructor for class etomica.lattice.LatticeHcp: Cubic hcp crystal with a lattice constant that gives a maximum-density structure for spheres of unit.
LatticeHcp(ISpace, double) - Constructor for class etomica.lattice.LatticeHcp
latticeIndex(IVector) - Method in class etomica.lattice.crystal.Primitive: Returns the index which would give the unit cell containing the given point if the index were passed to a the site method of a sufficiently large lattice that uses this primitive.
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.Primitive: Same as latticeIndex(Space.Vector), but gives index for periodic system with number of unit cells in each direction as given by the dimensions array.
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveBcc
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveBcc
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveCubic
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveCubic
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveFcc
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveFcc
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveGeneral
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveGeneral
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
latticeIndex(IVector) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
latticeIndex(IVector, int[]) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
latticeIndex(int) - Method in class etomica.lattice.RectangularLattice: Returns the lattice index given the 1-d array index; reverses the effect of arrayIndex method.
latticeIndex(int, int[]) - Method in class etomica.lattice.RectangularLattice
latticeIndex(IVector) - Method in class etomica.models.hexane.PrimitiveHexane
latticeIndex(IVector, int[]) - Method in class etomica.models.hexane.PrimitiveHexane
latticeNameHash - Variable in class etomica.modules.crystalviewer.LatticeEditor
latticeOffset - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
LatticeOrthorhombicHexagonal - Class in etomica.lattice: Lattice class for a hexagonal lattice composed of rectangular primitives with a 2-atom basis.
LatticeOrthorhombicHexagonal(ISpace) - Constructor for class etomica.lattice.LatticeOrthorhombicHexagonal
LatticeOrthorhombicHexagonal(ISpace, double) - Constructor for class etomica.lattice.LatticeOrthorhombicHexagonal
LatticePlane - Class in etomica.lattice: Class describing a plane through a lattice.
LatticePlane(Primitive, int[]) - Constructor for class etomica.lattice.LatticePlane
latticePlane - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
latticePlane() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
latticePlane - Variable in class etomica.modules.crystalviewer.CrystalViewer
latticePressure - Variable in class etomica.normalmode.MeterSolidDA
latticePressure - Variable in class etomica.normalmode.MeterSolidDACut
latticePressureDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
latticeScale - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
latticeScale - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
latticeScaling - Variable in class etomica.config.ConfigurationLattice.MyLattice
latticeScaling - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
latticeScaling - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
LatticeSum - Class in etomica.lattice
LatticeSum(SpaceLattice) - Constructor for class etomica.lattice.LatticeSum
LatticeSumCrystal - Class in etomica.lattice
LatticeSumCrystal(BravaisLatticeCrystal) - Constructor for class etomica.lattice.LatticeSumCrystal
LatticeSumCrystal.DataGroupLSC - Class in etomica.lattice: Helper class that encapsulates the complex basis-basis data in a manner that permits easy access to real and imaginary components for a given pair of basis elements.
LatticeSumCrystalMolecular - Class in etomica.models.nitrogen: Lattice sum crystal for molecular model
LatticeSumCrystalMolecular(BravaisLatticeCrystal, CoordinateDefinitionNitrogen, IBox) - Constructor for class etomica.models.nitrogen.LatticeSumCrystalMolecular
LatticeSumCrystalMolecular.DataGroupLSC - Class in etomica.models.nitrogen: Helper class that encapsulates the complex basis-basis data in a manner that permits easy access to real and imaginary components for a given pair of basis elements.
LatticeSumCrystalParacetamol - Class in etomica.paracetamol
LatticeSumCrystalParacetamol(BravaisLatticeCrystal) - Constructor for class etomica.paracetamol.LatticeSumCrystalParacetamol
LatticeSumCrystalParacetamol.DataGroupLSCParacetamol - Class in etomica.paracetamol: Helper class that encapsulates the complex basis-basis data in a manner that permits easy access to real and imaginary components for a given pair of basis elements.
LatticeSumMolecularCrystal - Class in etomica.normalmode
LatticeSumMolecularCrystal(IPotentialMaster, IBox, ISpace, int, Primitive) - Constructor for class etomica.normalmode.LatticeSumMolecularCrystal
LatticeSumMolecularCrystal.AtomicTensorAtomicPair - Interface in etomica.normalmode
latticeVectors - Variable in class etomica.lattice.crystal.Primitive
Launcher - Class in etomica.graph.engine
Launcher() - Constructor for class etomica.graph.engine.Launcher
Launcher.ConsoleWindow - Class in etomica.graph.engine
Launcher.ConsoleWindowRunnable - Class in etomica.graph.engine
lAvg - Variable in class etomica.data.AccumulatorAverageCollapsingLog
lcaocartoon - Static variable in class org.jmol.script.Token
lcex - Static variable in class etomica.potential.P2HydrogenPatkowski
lcex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
lcm(BigInteger, BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: The lowest common multiple
lcm(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Lowest common multiple of this with oth.
lcmDenom(Rational[]) - Static method in class etomica.veos.bigdecimal.Rational: Common lcm of the denominators of a set of rational values.
lcsp - Static variable in class etomica.potential.P2HydrogenPatkowski
lcsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
lData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
lDataInfo - Variable in class etomica.data.AccumulatorAverageCollapsingLog
ldegree() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Polynomial lower degree.
ldum - Variable in class etomica.potential.P2HydrogenPatkowski
ldum - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
leafAgentIterator - Variable in class etomica.potential.PotentialCalculationTorqueSum
leafAgentManager - Variable in class etomica.integrator.IntegratorRigidIterative
leafAgentManager - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
leafAgentManager - Variable in class etomica.potential.PotentialCalculationTorqueSum
leafAgentManager - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
leafAtoms - Variable in class etomica.potential.P2MoleculeMonatomic
leafAtomType - Variable in class etomica.species.SpeciesSpheres
leafAtomType - Variable in class etomica.species.SpeciesSpheresMono
leafIndex - Variable in class etomica.atom.Atom
leafIterator - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
leafIterator - Variable in class etomica.virial.MCMoveClusterRingRegrow
leafIterator - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
leafIterator - Variable in class etomica.virial.MCMoveClusterRingScale
leafList - Variable in class etomica.box.Box: List of leaf atoms in box
leafList - Variable in class etomica.graphics.ColorSchemeOverlap
leafList - Variable in class etomica.normalmode.P1ConstraintNbr
leafList - Variable in class etomica.normalmode.P1ConstraintNbrHcp
leafList - Variable in class etomica.potential.PotentialCalculationPressureTensor
leafType - Variable in class etomica.modules.interfacial.InterfacialSW
LEFT - Static variable in class etomica.graphics.DisplayBox
LEFT - Static variable in class etomica.graphics.DisplayPolytope
LEFT - Static variable in class etomica.util.Constants.Direction
left - Static variable in class org.jmol.script.Token
leftDifference(Quaternion) - Method in class org.jmol.util.Quaternion
leftmostBit(int) - Static method in class etomica.graph.traversal.BitmapUtils
legacyautobonding - Static variable in class org.jmol.script.Token
legendreP(int, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
legendreP(int, double) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
legendreP(int, double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
Length - Class in etomica.units: Dimension for all units of length.
length() - Method in class etomica.units.systems.CGS
length() - Method in class etomica.units.systems.LJ
length() - Method in class etomica.units.systems.MKS
length() - Method in class etomica.units.systems.UnitSystem
length() - Method in class etomica.units.systems.UnitSystem.Sim
length - Variable in class etomica.util.FastFourierTransform
length() - Method in class org.jmol.util.BitSet: Returns the "logical size" of this BitSet: the index of the highest set bit in the BitSet plus one.
length() - Method in class org.jmol.util.StringXBuilder
length() - Method in class org.jmol.util.Vector3f: Returns the length of this vector.
LengthAgent() - Constructor for class etomica.modules.chainequilibrium.AtomFilterChainLength.LengthAgent
LengthAgent() - Constructor for class etomica.modules.chainequilibrium.ColorSchemeRadical.LengthAgent
lengths - Variable in class org.jmol.util.Quadric
lengthSquared() - Method in class org.jmol.util.Vector3f: Returns the squared length of this vector.
lengthX - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
lengthY - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
lengthZ - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
LennardJones - Class in etomica.statmech: Implementation of some semi-empirical equations of state for the Lennard-Jones model.
LESS_THAN - Static variable in class etomica.compatibility.Feature
LEVEL - Static variable in class etomica.util.Debug: debugging level.
level - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
LEVEL_DEBUG - Static variable in class org.jmol.util.Logger
LEVEL_DEBUGHIGH - Static variable in class org.jmol.util.Logger
LEVEL_ERROR - Static variable in class org.jmol.util.Logger
LEVEL_FATAL - Static variable in class org.jmol.util.Logger
LEVEL_INFO - Static variable in class org.jmol.util.Logger
LEVEL_MAX - Static variable in class org.jmol.util.Logger
LEVEL_WARN - Static variable in class org.jmol.util.Logger
lex - Static variable in class etomica.potential.P2HydrogenPatkowski
lex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
lFill(StringXBuilder, String, String) - Static method in class org.jmol.util.TextFormat
Li - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
LIGHT_SPEED - Static variable in class etomica.util.Constants: The speed of light, in simulation units.
LIME - Static variable in class org.jmol.util.Colix
LimitType(String) - Constructor for class etomica.data.DataSourceUniform.LimitType
LINE - Static variable in class g3dsys.control.G3DSys
Line - Class in g3dsys.images
Line(G3DSys, short, Point3f, Point3f) - Constructor for class g3dsys.images.Line
Linear(double, double) - Constructor for class etomica.util.Function.Linear
LinearFit - Class in etomica.util.numerical: Class that performs a linear fit to x,y data, optionally taking weights associated with each data point.
LinearFit() - Constructor for class etomica.util.numerical.LinearFit
lineFigures - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
lines - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
LineSegment - Class in etomica.math.geometry: A geometrical line segment, a 1-dimensional polytope.
LineSegment(ISpace) - Constructor for class etomica.math.geometry.LineSegment
Link(IFunction, FunctionChain.Link) - Constructor for class etomica.util.FunctionChain.Link
linker - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
Linker(Object, EventManager.Linker, boolean) - Constructor for class etomica.util.EventManager.Linker
linp - Static variable in class etomica.potential.P2WaterPotentialsJankowski
linPSpan - Variable in class etomica.normalmode.MeterDDP
linPSpan - Variable in class etomica.normalmode.MeterDP
liquidColor - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
liquidFccCoexDensities(double) - Static method in class etomica.statmech.LennardJones: Returns the densities of coexisting (saturated) liquid and fcc phases (i.e., melting and freezing densities).
liquidFccCoexPressure(double) - Static method in class etomica.statmech.LennardJones: Returns the saturation pressure for fluid-fcc coexistence (i.e., the melting or freezing pressure).
liquidFilter - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
liquidFilter - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
liquidFilter - Variable in class etomica.modules.droplet.Droplet
liquidFilter - Variable in class etomica.modules.droplet.P2Cohesion
list - Variable in class etomica.atom.AtomSourceRandomLeaf
list - Variable in class etomica.atom.AtomSourceRandomSpecies
list - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple
list - Variable in class etomica.atom.iterator.MoleculeIteratorArrayListSimple
list - Variable in class etomica.compatibility.FeatureSet
list - Variable in class etomica.dimer.IntegratorDimerMin
list - Variable in class etomica.dimer.IntegratorDimerRT
list(Parser.Command) - Method in class etomica.graph.engine.Interpreter
list - Variable in class etomica.graph.model.GraphList
list - Variable in class etomica.potential.PotentialMaster.AtomIterator0
list - Variable in class etomica.potential.PotentialMaster.MoleculeIterator0
list - Static variable in class org.jmol.script.Token
list0 - Variable in class etomica.potential.PotentialMasterLrc
list1 - Variable in class etomica.dimer.IntegratorDimerRT
list2 - Variable in class etomica.dimer.IntegratorDimerRT
listdimensions() - Static method in class etomica.units.Lister
listener - Variable in class etomica.util.EventManager.Linker
ListenerGroup - Interface in etomica.listener
listeners - Variable in class etomica.data.DataSet
Lister - Class in etomica.units
Lister() - Constructor for class etomica.units.Lister
listLeaf0 - Variable in class etomica.potential.PotentialMasterLrc
listMin - Variable in class etomica.dimer.IntegratorDimerMin
listsPoint - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
listsPoint - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
listsPoint - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
listsPoint - Variable in class etomica.virial.MeterVirialExternalFieldOverlapRho
listsPoint - Variable in class etomica.virial.MeterVirialExternalFieldRho
listToUpdate - Variable in class etomica.integrator.IntegratorHard
listUnits() - Static method in class etomica.units.Lister
listUnitsInSystem(String) - Static method in class etomica.units.Lister
listUnitSystems() - Static method in class etomica.units.Lister
listValue(Token) - Static method in class org.jmol.script.ScriptVariable
Liter - Class in etomica.units: The liter unit of volume, equal to 1000 cm^3 or 0.001 m^3 or 10^27 A^3.
Liter() - Constructor for class etomica.units.Liter
LJ - Class in etomica.units.systems: Lennard-Jones system of units, such that all quantities are made dimensionless with respect to a characteristic size (sigma), energy (epsilon) and mass.
LJ() - Constructor for class etomica.units.systems.LJ: Constructs LJ unit system with default values of sigma, epsilon and mass each equal to unity.
LJ(double, double, double, boolean) - Constructor for class etomica.units.systems.LJ: Constructs LJ unit system with given values of sigma, epsilon, mass.
lj - Variable in class etomica.units.systems.LJ.LJUnit
LJ.LJUnit - Class in etomica.units.systems
LJMC - Class in etomica.interfacial: Simple Lennard-Jones molecular dynamics simulation in 3D
LJMC(double, String) - Constructor for class etomica.interfacial.LJMC
LJMC - Class in etomica.modules.ensembles
LJMC(Space) - Constructor for class etomica.modules.ensembles.LJMC
LJMC - Class in etomica.surfacetension
LJMC(ISpace, int, double, double) - Constructor for class etomica.surfacetension.LJMC
LJMC.LjMC3DParams - Class in etomica.interfacial
LJMC.LJMCParams - Class in etomica.surfacetension
LjMC3D - Class in etomica.liquidLJ: Simple Lennard-Jones molecular dynamics simulation in 3D
LjMC3D(int, double, double, double) - Constructor for class etomica.liquidLJ.LjMC3D
LjMc3D - Class in etomica.thermointegration: Simple Lennard-Jones molecular dynamics simulation in 3D
LjMc3D() - Constructor for class etomica.thermointegration.LjMc3D
LjMc3D.Applet - Class in etomica.thermointegration
LjMC3D.LjMC3DParams - Class in etomica.liquidLJ
LjMC3DParams() - Constructor for class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
LjMC3DParams() - Constructor for class etomica.freeenergy.npath.SimLJ.LjMC3DParams
LjMC3DParams() - Constructor for class etomica.interfacial.LJMC.LjMC3DParams
LjMC3DParams() - Constructor for class etomica.liquidLJ.LjMC3D.LjMC3DParams
LJMCGraphic - Class in etomica.modules.ensembles
LJMCGraphic(LJMC, Space) - Constructor for class etomica.modules.ensembles.LJMCGraphic
LJMCGraphic.Applet - Class in etomica.modules.ensembles
LJMCParams() - Constructor for class etomica.metastable.LJmuVT.LJMCParams
LJMCParams() - Constructor for class etomica.metastable.LJNPT.LJMCParams
LJMCParams() - Constructor for class etomica.metastable.LJNVT.LJMCParams
LJMCParams() - Constructor for class etomica.surfacetension.LJMC.LJMCParams
LJMD - Class in etomica.interfacial: Simple Lennard-Jones molecular dynamics simulation in 3D
LJMD(double, double, boolean, double, double, double, int, int, String) - Constructor for class etomica.interfacial.LJMD
Ljmd - Class in etomica.modules.ljmd
Ljmd(Space) - Constructor for class etomica.modules.ljmd.Ljmd
LJMD.LJMDParams - Class in etomica.interfacial
LjMd2D - Class in etomica.simulation.prototypes: Simple Lennard-Jones molecular dynamics simulation in 2D
LjMd2D() - Constructor for class etomica.simulation.prototypes.LjMd2D
LjMd3D - Class in etomica.liquidLJ: Simple Lennard-Jones molecular dynamics simulation in 3D
LjMd3D(int, double, double, double, double, double, double, int, IFunction, boolean) - Constructor for class etomica.liquidLJ.LjMd3D
LjMd3D - Class in etomica.simulation.prototypes: Simple Lennard-Jones molecular dynamics simulation in 3D
LjMd3D() - Constructor for class etomica.simulation.prototypes.LjMd3D
LjMd3D.Applet - Class in etomica.simulation.prototypes
LjMd3D.DataProcessorCorrection - Class in etomica.liquidLJ
LjMd3D.DataProcessorReweight - Class in etomica.liquidLJ
LjMd3D.LjMd3DParams - Class in etomica.liquidLJ
LjMd3D.ValueCache - Class in etomica.liquidLJ
LjMd3D.VolumeBias - Class in etomica.liquidLJ
LjMd3DParams() - Constructor for class etomica.liquidLJ.LjMd3D.LjMd3DParams
LjMd3DParams() - Constructor for class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
LJMD3DThreaded - Class in etomica.threaded.atom: Simple Lennard-Jones Monte Carlo simulation in 3D.
LJMD3DThreaded() - Constructor for class etomica.threaded.atom.LJMD3DThreaded
LJMD3DThreaded(int, int) - Constructor for class etomica.threaded.atom.LJMD3DThreaded
LJMD3DThreaded - Class in etomica.threaded.domain: Simple Lennard-Jones Monte Carlo simulation in 3D.
LJMD3DThreaded() - Constructor for class etomica.threaded.domain.LJMD3DThreaded
LJMD3DThreaded(int, int) - Constructor for class etomica.threaded.domain.LJMD3DThreaded
LJMD3DThreadedforCluster - Class in etomica.threaded.atom
LJMD3DThreadedforCluster() - Constructor for class etomica.threaded.atom.LJMD3DThreadedforCluster
LJMD3DThreadedforCluster - Class in etomica.threaded.domain
LJMD3DThreadedforCluster() - Constructor for class etomica.threaded.domain.LJMD3DThreadedforCluster
LjMd3Dv2y - Class in etomica.liquidLJ: Simple Lennard-Jones molecular dynamics simulation in 3D
LjMd3Dv2y() - Constructor for class etomica.liquidLJ.LjMd3Dv2y
LjMd3Dv2y.LjMd3DParams - Class in etomica.liquidLJ
LjmdGraphic - Class in etomica.modules.ljmd
LjmdGraphic(Ljmd, Space) - Constructor for class etomica.modules.ljmd.LjmdGraphic
LjmdGraphic.Applet - Class in etomica.modules.ljmd
LjmdGraphic.DataProcessorTensorTrace - Class in etomica.modules.ljmd: Inner class to find the total pressure of the system from the pressure tensor.
LJMDParams() - Constructor for class etomica.interfacial.LJMD.LJMDParams
LJMDParams() - Constructor for class etomica.mappedvirial.MappedU.LJMDParams
LJMDParams() - Constructor for class etomica.mappedvirial.MappedVirialLJ.LJMDParams
LJMDParams() - Constructor for class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
LJmuVT - Class in etomica.metastable
LJmuVT(ISpace, int, double, double, double, double, int[]) - Constructor for class etomica.metastable.LJmuVT
LJmuVT.LJMCParams - Class in etomica.metastable
LJNPT - Class in etomica.metastable
LJNPT(ISpace, int, double, double, double, double, int[]) - Constructor for class etomica.metastable.LJNPT
LJNPT.LJMCParams - Class in etomica.metastable
LJNVT - Class in etomica.metastable
LJNVT(ISpace, int, double, double, double, int[]) - Constructor for class etomica.metastable.LJNVT
LJNVT.LJMCParams - Class in etomica.metastable
LJParams() - Constructor for class etomica.normalmode.SimLJVacancy.LJParams
LJQB2 - Class in etomica.modules.vle: Class that provides method to compute the 2nd virial coefficient for the Lennard-Jones + point-quadrupole model potential.
LJQB2() - Constructor for class etomica.modules.vle.LJQB2
LJTSRefLJ - Class in etomica.virial.simulations: The direct-sampling formulation of Mayer-Sampling Monte Carlo is employed to compute a virial coefficient of truncated-and-shifted Lennard Jones (LJTS), at a particular temperature.
LJTSRefLJ() - Constructor for class etomica.virial.simulations.LJTSRefLJ
LJTSRefLJ.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
LJUnit(LJ) - Constructor for class etomica.units.systems.LJ.LJUnit: Unit must provide instance of LJ unit system at construction.
LJVacancyMin - Class in etomica.normalmode
LJVacancyMin(Space, int, double, double, boolean) - Constructor for class etomica.normalmode.LJVacancyMin
LJVacancyMin.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
LJVacancyMin.VectorForce - Class in etomica.normalmode
ll - Static variable in class etomica.potential.P2O2Bartolomei
lla - Static variable in class etomica.potential.P2O2Bartolomei
llb - Static variable in class etomica.potential.P2O2Bartolomei
llex - Static variable in class etomica.potential.P2HydrogenPatkowski
llex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
llsp - Static variable in class etomica.potential.P2HydrogenPatkowski
llsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
lnAlpha - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
lnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
lnAlpha - Variable in class etomica.overlap.DataOverlap
lnAlphaDiff - Variable in class etomica.overlap.DataOverlap
lnbias - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
lnFactorial(int) - Static method in class etomica.math.SpecialFunctions
lnfXi - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
lnfXi - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
lnfXi - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
lnfXi - Variable in class etomica.virial.cluster.VirialDiagrams
lnfXi - Variable in class etomica.virial.cluster.VirialDiagramsMix
lnfXi - Variable in class etomica.virial.cluster.VirialDiagramsMix2
lnfXi - Variable in class etomica.virial.cluster.VirialDiagramsPT
lnfXi - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
lnfXi - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
lnGamma(double) - Static method in class etomica.math.SpecialFunctions: Returns the ln(gamma), the natural logarithm of the gamma function.
lnN - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
lnN - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
lnRatio - Variable in class etomica.overlap.DataOverlap
lnStdev - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
lnValue() - Method in class etomica.veos.BigValue: Returns logarithm of the value represented by the instance.
lnValue() - Method in interface etomica.veos.IBigValue: Returns logarithm of the value represented by the instance.
lnValue() - Method in class etomica.veos.MyBigDecimal: Returns logarithm of the value represented by the instance.
load - Variable in class etomica.modules.materialfracture.PotentialCalculationForceStress
LOAD_ATOM_DATA_TYPES - Static variable in class org.jmol.viewer.JmolConstants
loadatomdatatolerance - Static variable in class org.jmol.script.Token
loadConfiguration(String) - Method in class etomica.kmc.IntegratorKMC
loadConfiguration(String) - Method in class etomica.kmc.IntegratorKMCCluster
loadformat - Static variable in class org.jmol.script.Token
loadligandformat - Static variable in class org.jmol.script.Token
LocalFilter - Class in etomica.graph.iterators.filters
LocalFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.LocalFilter
localizableSupport - Static variable in class etomica.graph.view.rasterizer.Messages: The localizable support for the error messages.
localVisit(byte) - Method in class etomica.graph.traversal.AbstractTraversal
log() - Method in class etomica.math.Complex: Principal branch of the Complex logarithm of this Complex number.
log - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
Log() - Constructor for class etomica.util.Function.Log
log(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The natural logarithm.
log(int, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The natural logarithm.
log(Rational, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The natural logarithm.
log(PrintStream, int, String, Throwable) - Method in class org.jmol.util.DefaultLogger: Method to output a log.
log10Steps - Variable in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
log10Steps - Variable in class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
log10Steps - Variable in class etomica.virial.simulations.ReeHooverMC.VirialParam
logcommands - Static variable in class org.jmol.script.Token
logfile - Static variable in class org.jmol.script.Token
Logger - Class in org.jmol.util: Logger mechanism.
Logger() - Constructor for class org.jmol.util.Logger
LoggerInterface - Interface in org.jmol.util: Interface used for the logging mechanism.
loggestures - Static variable in class org.jmol.script.Token
loglevel - Static variable in class org.jmol.script.Token
logLevel() - Static method in class org.jmol.util.Logger: Indicates if the level is logged.
logWarn - Variable in class etomica.graphics.DisplayPlot
LONG_MASK - Static variable in interface etomica.graph.model.Bitmap
LONG_ONE - Static variable in interface etomica.graph.model.Bitmap
LONG_ZERO - Static variable in interface etomica.graph.model.Bitmap
longH2H2(double, double, double, double, double[]) - Method in class etomica.potential.P2HydrogenPatkowski
longH2H2(double, double, double, double, double[]) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
longOffset(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit bitSize() - 1 of bitmap[size()-1].
lookUp - Static variable in class etomica.space3d.Vector3D
lookupSpecialAtomID(String) - Static method in class org.jmol.viewer.JmolConstants
lout - Static variable in class etomica.potential.P2WaterPotentialsJankowski
low - Variable in class etomica.graph.traversal.Biconnected
LOWER_MASK - Static variable in class etomica.util.RandomMersenneTwister
lowest(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: This will tell you what the lowest open space is in atom a
lowest(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: This will tell you what the lowest open space is in atom a
lp - Static variable in class etomica.math.SpecialFunctions
lrcAtomsPerMolecule - Variable in class etomica.potential.Potential0Lrc
lrcMaster() - Method in interface etomica.api.IPotentialMaster: Returns the object that oversees the long-range correction zero-body potentials.
lrcMaster - Variable in class etomica.potential.PotentialMaster
lrcMaster() - Method in class etomica.potential.PotentialMaster
lsb() - Method in interface etomica.graph.model.Bitmap
lsb() - Method in class etomica.graph.model.impl.AbstractBitmap
lsp - Static variable in class etomica.potential.P2HydrogenPatkowski
lsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
lsPosition - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
lsPosition - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
lsPosition - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
lsPosition - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
lsPosition - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
lsPosition - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
lsPosition - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
lsPosition - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
lsPosition - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
lsPosition - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
lSums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
lub() - Method in interface etomica.graph.model.Bitmap
lub() - Method in class etomica.graph.model.impl.AbstractBitmap
LuminousIntensity - Class in etomica.units: The dimension for luminous intensity.
luminousIntensity() - Method in class etomica.units.systems.UnitSystem
lx - Variable in class etomica.util.numerical.AkimaSplineSmoother
Lxy - Variable in class etomica.interfacial.ConfigurationLammps
Lxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
Lxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
Lxyz - Variable in class etomica.meam.PotentialFeEAM_LS
Lxyz - Variable in class etomica.potential.EwaldSummation
Lxyz - Variable in class etomica.potential.Potential2SoftSphericalLS
ly - Variable in class etomica.util.numerical.AkimaSplineSmoother

M

M - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
m - Variable in class etomica.lattice.IndexIteratorIncreasing
m - Variable in class etomica.meam.PotentialFeEAM
m - Variable in class etomica.util.numerical.AkimaSpline
m - Variable in class etomica.util.numerical.AkimaSplineSmoother
M - Variable in class etomica.util.numerical.FittingFunctionNonLinear
M - Variable in class etomica.util.numerical.FittingFunctionNonLinearB
M - Static variable in class etomica.util.RandomMersenneTwister
m00 - Variable in class org.jmol.util.Matrix3f: The first element of the first row.
m00 - Variable in class org.jmol.util.Matrix4f: The first element of the first row.
m01 - Variable in class org.jmol.util.Matrix3f: The second element of the first row.
m01 - Variable in class org.jmol.util.Matrix4f: The second element of the first row.
m02 - Variable in class org.jmol.util.Matrix3f: third element of the first row.
m02 - Variable in class org.jmol.util.Matrix4f: third element of the first row.
m03 - Variable in class org.jmol.util.Matrix4f: The fourth element of the first row.
m10 - Variable in class org.jmol.util.Matrix3f: The first element of the second row.
m10 - Variable in class org.jmol.util.Matrix4f: The first element of the second row.
m11 - Variable in class org.jmol.util.Matrix3f: The second element of the second row.
m11 - Variable in class org.jmol.util.Matrix4f: The second element of the second row.
m12 - Variable in class org.jmol.util.Matrix3f: The third element of the second row.
m12 - Variable in class org.jmol.util.Matrix4f: The third element of the second row.
m13 - Variable in class org.jmol.util.Matrix4f: The fourth element of the second row.
m20 - Variable in class org.jmol.util.Matrix3f: The first element of the third row.
m20 - Variable in class org.jmol.util.Matrix4f: The first element of the third row.
m21 - Variable in class org.jmol.util.Matrix3f: The second element of the third row.
m21 - Variable in class org.jmol.util.Matrix4f: The second element of the third row.
m22 - Variable in class org.jmol.util.Matrix3f: The third element of the third row.
m22 - Variable in class org.jmol.util.Matrix4f: The third element of the third row.
m23 - Variable in class org.jmol.util.Matrix4f: The fourth element of the third row.
m2s(IMoleculeList) - Static method in class etomica.virial.ClusterSumMultibody
m30 - Variable in class org.jmol.util.Matrix4f: The first element of the fourth row.
m31 - Variable in class org.jmol.util.Matrix4f: The second element of the fourth row.
m32 - Variable in class org.jmol.util.Matrix4f: The third element of the fourth row.
m33 - Variable in class org.jmol.util.Matrix4f: The fourth element of the fourth row.
ma - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
ma - Variable in class etomica.util.numerical.NonLinearCurveFitting
MacrostateManager - Interface in etomica.tmmc: Interface for class that defines the macrostates.
madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JmolConstants
MAGENTA - Static variable in class org.jmol.util.Colix
main(String[]) - Static method in class etomica.AlkaneEH.CH4NVT
main(String[]) - Static method in class etomica.AlkaneEH.DHS_NVT
main(String[]) - Static method in class etomica.AlkaneEH.DLJ_NVT_1site
main(String[]) - Static method in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
main(String[]) - Static method in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid
main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp
main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite
main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp
main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal
main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite
main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling
main(String[]) - Static method in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
main(String[]) - Static method in class etomica.association.TestLJAssociationMC3D_NPT
main(String[]) - Static method in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
main(String[]) - Static method in class etomica.association.TestLJAssociationMC3D_NVTOld
main(String[]) - Static method in class etomica.conjugategradient.ConjugateGradients
main(String[]) - Static method in class etomica.conjugategradient.PreconditionedConjugateGradient
main(String[]) - Static method in class etomica.conjugategradient.SteepestDescent
main(String[]) - Static method in class etomica.conjugategradient.TestFiniteDifferenceDerivative
main(String[]) - Static method in class etomica.conjugategradient.TestNonLinearConjugateGradients
main(String[]) - Static method in class etomica.data.AccumulatorAverageCollapsingLog
main(String[]) - Static method in class etomica.data.DataSourceUniform: Main method to demonstrate and check class.
main(String[]) - Static method in class etomica.densityofstate.CopyOfOrthogonalPolynomial
main(String[]) - Static method in class etomica.densityofstate.DensityOfState
main(String[]) - Static method in class etomica.densityofstate.DensityOfStatesPolynomial
main(String[]) - Static method in class etomica.densityofstate.FerrenbergSwendsen
main(String[]) - Static method in class etomica.densityofstate.OrthogonalPolynomial
main(String[]) - Static method in class etomica.dielectric.DHS_NVT
main(String[]) - Static method in class etomica.dielectric.DLJ_NVT_1site
main(String[]) - Static method in class etomica.dielectric.TIP4P_NVT
main(String[]) - Static method in class etomica.dimer.EnergyMap
main(String[]) - Static method in class etomica.dimer.EnergyMapCluster
main(String[]) - Static method in class etomica.dimer.SimDimerLJadatom
main(String[]) - Static method in class etomica.dimer.SimDimerLJadatomCluster
main(String[]) - Static method in class etomica.dimer.SimDimerLJgb
main(String[]) - Static method in class etomica.dimer.SimDimerMEAMadatom
main(String[]) - Static method in class etomica.dimer.SimDimerMEAMadatomCluster
main(String[]) - Static method in class etomica.dimer.SimDimerMEAMGB
main(String[]) - Static method in class etomica.dimer.SimDimerMEAMGBCluster
main(String[]) - Static method in class etomica.eigenstuff.ReaderIn
main(String[]) - Static method in class etomica.freeenergy.npath.SimIdealGas
main(String[]) - Static method in class etomica.freeenergy.npath.SimLJ
main(String[]) - Static method in class etomica.gaussianwork.SimOverlapMultiHarmonic
main(String[]) - Static method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
main(String[]) - Static method in class etomica.graph.engine.Launcher
main(String[]) - Static method in class etomica.graph.operations.DropOrphanNodes
main(String[]) - Static method in class etomica.graph.property.FFTDecomposition
main(String[]) - Static method in class etomica.graph.property.IsFFT
main(String[]) - Static method in class etomica.graph.util.GraphNumber
Main - Class in etomica.graph.view.rasterizer: Handles command line parameters to configure the SVGConverter and rasterizer images.
Main(String[]) - Constructor for class etomica.graph.view.rasterizer.Main
main(String[]) - Static method in class etomica.graph.view.rasterizer.Main
main(String[]) - Static method in class etomica.graphics.ColorScheme
main(String[]) - Static method in class etomica.graphics.DeviceButton: Method to demonstrate and test the use of this class.
main(String[]) - Static method in class etomica.graphics.DeviceNSelector
main(String[]) - Static method in class etomica.graphics.DeviceTable: main method to demonstrate and test this class.
main(String[]) - Static method in class etomica.graphics.DeviceThermoSelector
main(String[]) - Static method in class etomica.graphics.DeviceThermoSlider
main(String[]) - Static method in class etomica.graphics.DeviceToggleButton: Method to demonstrate and test the use of this class.
main(String[]) - Static method in class etomica.graphics.DeviceTrioControllerButton: main method to show how to work with this class
main(String[]) - Static method in class etomica.graphics.DisplayTable: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.graphics.DisplayTextBoxesCAE
main(String[]) - Static method in class etomica.graphics.SimulationGraphic: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.integrator.IntegratorRigidIterative
main(String[]) - Static method in class etomica.interfacial.LJMC
main(String[]) - Static method in class etomica.interfacial.LJMD
main(String[]) - Static method in class etomica.kmc.SimKMCLJadatom
main(String[]) - Static method in class etomica.kmc.SimKMCmaster
main(String[]) - Static method in class etomica.kmc.SimKMCMEAMadatom
main(String[]) - Static method in class etomica.kmc.SimKMCworker
main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveFcc
main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveHexagonal
main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveMonoclinic
main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveTriclinic
main(String[]) - Static method in class etomica.lattice.IndexIteratorIncreasing
main(String[]) - Static method in class etomica.lattice.IndexIteratorRectangular: main method to test and demonstrate class.
main(String[]) - Static method in class etomica.lattice.IndexIteratorReflecting: Method to test and demonstrate class.
main(String[]) - Static method in class etomica.lattice.IndexIteratorTriangular: Method to test and demonstrate class.
main(String[]) - Static method in class etomica.lattice.IndexIteratorTriangularPermutations: Method to test and demonstrate class.
main(String[]) - Static method in class etomica.lattice.RectangularLatticeNbrIteratorAdjacent: Method to test the neighbor iterator.
main(String[]) - Static method in class etomica.lattice.RectangularLatticeNbrIteratorSquare: Method to test the neighbor iterator.
main(String[]) - Static method in class etomica.liquidLJ.LjMC3D
main(String[]) - Static method in class etomica.liquidLJ.LjMd3D
main(String[]) - Static method in class etomica.liquidLJ.LjMd3Dv2y
main(String[]) - Static method in class etomica.mappedvirial.MappedU
main(String[]) - Static method in class etomica.mappedvirial.MappedUpotential
main(String[]) - Static method in class etomica.mappedvirial.MappedVirialLJ
main(String[]) - Static method in class etomica.mappedvirial.MappedVirialLJVGr
main(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedVirial
main(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
main(String[]) - Static method in class etomica.math.discrete.CombinationIterator
main(String[]) - Static method in class etomica.math.discrete.FixedSumIterator
main(String[]) - Static method in class etomica.math.discrete.PermutationDegenerateIterator
main(String[]) - Static method in class etomica.math.discrete.PermutationIterator
main(String[]) - Static method in class etomica.math.Gamma
main(String[]) - Static method in class etomica.math.geometry.LineSegment
main(String[]) - Static method in class etomica.math.geometry.Plane
main(String[]) - Static method in class etomica.math.linearalgebra.GaussJordanElimination
main(String[]) - Static method in class etomica.math.SpecialFunctions
main(String[]) - Static method in class etomica.meam.EFSTungsten
main(String[]) - Static method in class etomica.meam.MEAM_3DMDwithGB
main(String[]) - Static method in class etomica.meam.MEAM_3DMDwithSnAgGB
main(String[]) - Static method in class etomica.meam.MEAM_3DMDwithSnCuGB
main(String[]) - Static method in class etomica.meam.MEAM_MC
main(String[]) - Static method in class etomica.meam.MEAMMd3D
main(String[]) - Static method in class etomica.meam.MEAMMd3DforCluster
main(String[]) - Static method in class etomica.metastable.LJmuVT
main(String[]) - Static method in class etomica.metastable.LJNPT
main(String[]) - Static method in class etomica.metastable.LJNVT
main(String[]) - Static method in class etomica.models.clathrates.ClathrateHarmonicFE
main(String[]) - Static method in class etomica.models.clathrates.MinimizationTIP4P
main(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
main(String[]) - Static method in class etomica.models.co2.P2CO2Hellmann
main(String[]) - Static method in class etomica.models.co2.PNCO2GCPM
main(String[]) - Static method in class etomica.models.co2.PNGCPM
main(String[]) - Static method in class etomica.models.hexane.HexaneVolumeFraction
main(String[]) - Static method in class etomica.models.hexane.SimHarmonicHexane
main(String[]) - Static method in class etomica.models.hexane.TestHexane
main(String[]) - Static method in class etomica.models.hexane.TestHexaneCBMCOnly
main(String[]) - Static method in class etomica.models.hexane.TestHexaneFileConfig
main(String[]) - Static method in class etomica.models.hexane.TestHexaneHarmonic
main(String[]) - Static method in class etomica.models.hexane.TestSetToUHexane
main(String[]) - Static method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
main(String[]) - Static method in class etomica.models.nitrogen.FindTransitionTemperature
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelLatticeSum
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelLatticeSum
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
main(String[]) - Static method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
main(String[]) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
main(String[]) - Static method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
main(String[]) - Static method in class etomica.models.nitrogen.SimDirectBetaN2RP
main(String[]) - Static method in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
main(String[]) - Static method in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
main(String[]) - Static method in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapBetaN2RP
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapBetaN2TP
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.SimulationBetaNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
main(String[]) - Static method in class etomica.models.nitrogen.SimulationGammaNitrogenModel
main(String[]) - Static method in class etomica.models.nitrogen.TestRotationVector
main(String[]) - Static method in class etomica.models.oneDHardRods.DoubleIntegral
main(String[]) - Static method in class etomica.models.oneDHardRods.DoubleIntegralEtas
main(String[]) - Static method in class etomica.models.oneDHardRods.HarmonicCrystalSsFccBigCellNxy
main(String[]) - Static method in class etomica.models.oneDHardRods.HarmonicCrystalSsFccDoubleSize
main(String[]) - Static method in class etomica.models.oneDHardRods.MakeData
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDegFreeBinning
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDegreeFreedom
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDegreeFreedom3D
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImage
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImage1D
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
main(String[]) - Static method in class etomica.models.oneDHardRods.SimExtensiveTest
main(String[]) - Static method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
main(String[]) - Static method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
main(String[]) - Static method in class etomica.models.oneDHardRods.SimOverlapSsNxy
main(String[]) - Static method in class etomica.models.oneDHardRods.SimWidomMode
main(String[]) - Static method in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
main(String[]) - Static method in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
main(String[]) - Static method in class etomica.models.rowley.DimerApproach
main(String[]) - Static method in class etomica.models.rowley.MassProductionVirialRowleyAlcohol
main(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
main(String[]) - Static method in class etomica.models.water.TestEwaldTIP4PWater
main(String[]) - Static method in class etomica.modules.adsorption.Adsorption
main(String[]) - Static method in class etomica.modules.adsorption.AdsorptionGraphic
main(String[]) - Static method in class etomica.modules.catalysis.Catalysis
main(String[]) - Static method in class etomica.modules.catalysis.CatalysisGraphic
main(String[]) - Static method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
main(String[]) - Static method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
main(String[]) - Static method in class etomica.modules.colloid.ColloidGraphic
main(String[]) - Static method in class etomica.modules.colloid.ColloidSim
main(String[]) - Static method in class etomica.modules.crystalviewer.CrystalViewer
main(String[]) - Static method in class etomica.modules.dcvgcmd.DCVGCMDGraphic
main(String[]) - Static method in class etomica.modules.droplet.Droplet
main(String[]) - Static method in class etomica.modules.droplet.DropletAtomic
main(String[]) - Static method in class etomica.modules.droplet.DropletAtomicGraphic
main(String[]) - Static method in class etomica.modules.droplet.DropletGraphic
main(String[]) - Static method in class etomica.modules.ensembles.LJMC
main(String[]) - Static method in class etomica.modules.ensembles.LJMCGraphic
main(String[]) - Static method in class etomica.modules.entropylottery.EntropyLottery
main(String[]) - Static method in class etomica.modules.entropylottery.EntropyLotteryGraphic
main(String[]) - Static method in class etomica.modules.insertion.Insertion
main(String[]) - Static method in class etomica.modules.insertion.InsertionGraphic
main(String[]) - Static method in class etomica.modules.interfacial.FitTanh
main(String[]) - Static method in class etomica.modules.interfacial.InterfacialSW
main(String[]) - Static method in class etomica.modules.interfacial.InterfacialSWGraphic
main(String[]) - Static method in class etomica.modules.joulethomson.JouleThomson
main(String[]) - Static method in class etomica.modules.joulethomson.JouleThomsonSim
main(String[]) - Static method in class etomica.modules.ljmd.Ljmd
main(String[]) - Static method in class etomica.modules.ljmd.LjmdGraphic
main(String[]) - Static method in class etomica.modules.materialfracture.MaterialFractureGraphic: /* main method
main(String[]) - Static method in class etomica.modules.mu.Mu
main(String[]) - Static method in class etomica.modules.mu.MuGraphic
main(String[]) - Static method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
main(String[]) - Static method in class etomica.modules.multiharmonic.MultiharmonicGraphic
main(String[]) - Static method in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
main(String[]) - Static method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
main(String[]) - Static method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
main(String[]) - Static method in class etomica.modules.osmosis.Osmosis
main(String[]) - Static method in class etomica.modules.osmosis.OsmosisSim
main(String[]) - Static method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
main(String[]) - Static method in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
main(String[]) - Static method in class etomica.modules.render.ParseObj
main(String[]) - Static method in class etomica.modules.render.RenderMDGraphic
main(String[]) - Static method in class etomica.modules.rheology.RheologyGraphic
main(String[]) - Static method in class etomica.modules.rheology.SimulationRheology
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosis
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisGraphic
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisWater
main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
main(String[]) - Static method in class etomica.modules.sam.Sam
main(String[]) - Static method in class etomica.modules.sam.SamGraphic
main(String[]) - Static method in class etomica.modules.swmd.Swmd
main(String[]) - Static method in class etomica.modules.swmd.SwmdGraphic
main(String[]) - Static method in class etomica.modules.vle.B2Fit
main(String[]) - Static method in class etomica.modules.vle.DeviceThermoSliderGEMC
main(String[]) - Static method in class etomica.modules.vle.LJQB2
main(String[]) - Static method in class etomica.modules.vle.VLE
main(String[]) - Static method in class etomica.modules.vle.VLESim
main(String[]) - Static method in class etomica.normalmode.ArrayA2B
main(String[]) - Static method in class etomica.normalmode.ArrayB2A
main(String[]) - Static method in class etomica.normalmode.CalcHarmonicA
main(String[]) - Static method in class etomica.normalmode.DeviceCellNum3DSlider
main(String[]) - Static method in class etomica.normalmode.DeviceCellNumXYSlider
main(String[]) - Static method in class etomica.normalmode.DeviceEigenvaluesSlider
main(String[]) - Static method in class etomica.normalmode.DeviceWaveVectorSlider
main(String[]) - Static method in class etomica.normalmode.HarmonicCrystal
main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSoftSphereBCC
main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSoftSphereFCC
main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSoftSphereHCP
main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSsFccNxy
main(String[]) - Static method in class etomica.normalmode.HessianDB
main(String[]) - Static method in class etomica.normalmode.HessianFromFile
main(String[]) - Static method in class etomica.normalmode.HSDimerNPT: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.normalmode.HSNPT: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.normalmode.HTTPSoftSphereApplet
main(String[]) - Static method in class etomica.normalmode.LJVacancyMin
main(String[]) - Static method in class etomica.normalmode.MeterHarmonicEnergy
main(String[]) - Static method in class etomica.normalmode.MinimizeHCP
main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay1D
main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay2D
main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay3D
main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
main(String[]) - Static method in class etomica.normalmode.NormalModeEigenGetter
main(String[]) - Static method in class etomica.normalmode.NormalModes1DHR
main(String[]) - Static method in class etomica.normalmode.NormalModes3D
main(String[]) - Static method in class etomica.normalmode.nptdemo.HSNPT2DGraphic: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.normalmode.SimBennet
main(String[]) - Static method in class etomica.normalmode.SimCalcJ
main(String[]) - Static method in class etomica.normalmode.SimCalcS
main(String[]) - Static method in class etomica.normalmode.SimCalcSLJ
main(String[]) - Static method in class etomica.normalmode.SimCalcSMorse
main(String[]) - Static method in class etomica.normalmode.SimCalcSSoftSphere2D
main(String[]) - Static method in class etomica.normalmode.SimCalcSSoftSphereFCC
main(String[]) - Static method in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
main(String[]) - Static method in class etomica.normalmode.SimEinStep1
main(String[]) - Static method in class etomica.normalmode.SimEinStep1HCP
main(String[]) - Static method in class etomica.normalmode.SimEinStep2
main(String[]) - Static method in class etomica.normalmode.SimEinStep2HCP
main(String[]) - Static method in class etomica.normalmode.SimFluidSoftSphere
main(String[]) - Static method in class etomica.normalmode.SimHarmonic
main(String[]) - Static method in class etomica.normalmode.SimHarmonicUmbrella
main(String[]) - Static method in class etomica.normalmode.SimHSMDVacancy
main(String[]) - Static method in class etomica.normalmode.SimLJHTTISuper
main(String[]) - Static method in class etomica.normalmode.SimLJHTTISuperHCP
main(String[]) - Static method in class etomica.normalmode.SimLJVacancy
main(String[]) - Static method in class etomica.normalmode.SimModesJ
main(String[]) - Static method in class etomica.normalmode.SimOverlap
main(String[]) - Static method in class etomica.normalmode.SimOverlapLJ
main(String[]) - Static method in class etomica.normalmode.SimOverlapLJModule
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphere
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereDP
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereEin
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereHCP
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereReweighting
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereSoftness
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereTP
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereTPHCP
main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
main(String[]) - Static method in class etomica.normalmode.SimOverlapSSnxy
main(String[]) - Static method in class etomica.normalmode.SimTarget
main(String[]) - Static method in class etomica.normalmode.SimTargetUmbrella
main(String[]) - Static method in class etomica.normalmode.SimUmbrella
main(String[]) - Static method in class etomica.normalmode.SimUmbrellaSoftSphere
main(String[]) - Static method in class etomica.normalmode.SoftSphereSolidEOS
main(String[]) - Static method in class etomica.normalmode.SoftSphereSolidEOSCalculator
main(String[]) - Static method in class etomica.normalmode.WaveVectorFactory1D
main(String[]) - Static method in class etomica.normalmode.WaveVectorFactory2D
main(String[]) - Static method in class etomica.normalmode.WaveVectorFactoryFcc
main(String[]) - Static method in class etomica.normalmode.WaveVectorFactorySimple
main(String[]) - Static method in class etomica.paracetamol.HarmonicCrystalMonoclinic
main(String[]) - Static method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTIEquilibration
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTISimCalcS
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTIEquilibration
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTISimCalcS
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
main(String[]) - Static method in class etomica.paracetamol.MDParacetamolMonoclinic: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.paracetamol.MDParacetamolOrthorhombic: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.paracetamol.NormalModeEigenGetter
main(String[]) - Static method in class etomica.parser.ParserLAMMPS
main(String[]) - Static method in class etomica.potential.P2ArgonSlavicekEtAl2003
main(String[]) - Static method in class etomica.potential.P2ArgonTangAndToennies2003
main(String[]) - Static method in class etomica.potential.P2DiscreteFeynmanHibbs
main(String[]) - Static method in class etomica.potential.P2EffectiveFeynmanHibbs
main(String[]) - Static method in class etomica.potential.P2HePCKLJS
main(String[]) - Static method in class etomica.potential.P2HydrogenHinde
main(String[]) - Static method in class etomica.potential.P2HydrogenPatkowski
main(String[]) - Static method in class etomica.potential.P2HydrogenPatkowskiIso
main(String[]) - Static method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
main(String[]) - Static method in class etomica.potential.P2NitrogenHellmann
main(String[]) - Static method in class etomica.potential.P2O2Bartolomei
main(String[]) - Static method in class etomica.potential.P2QChemInterpolated
main(String[]) - Static method in class etomica.potential.P2SoftSphericalTruncatedSwitched
main(String[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
main(String[]) - Static method in class etomica.potential.P3AdditiveQChem
main(String[]) - Static method in class etomica.potential.P3BondAngle
main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHe
main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHeOrig
main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHeSimplified
main(String[]) - Static method in class etomica.potential.P3HydrogenATM
main(String[]) - Static method in class etomica.potential.P3HydrogenManzhos
main(String[]) - Static method in class etomica.potential.P3Induction
main(String[]) - Static method in class etomica.potential.P3QChem
main(String[]) - Static method in class etomica.potential.P4BondTorsion
main(String[]) - Static method in class etomica.potential.P4BondTorsionAlkaneXCCH
main(String[]) - Static method in class etomica.potential.P4BondTorsionOPLS
main(String[]) - Static method in class etomica.potential.PotentialEmul
main(String[]) - Static method in class etomica.rotation.DipoleBox
main(String[]) - Static method in class etomica.rotation.DipoleBoxMatrix
main(String[]) - Static method in class etomica.rotation.IntegratorVelocityVerletQuaternion
main(String[]) - Static method in class etomica.rotation.P2LJDipole
main(String[]) - Static method in class etomica.rotation.SingleDipole
main(String[]) - Static method in class etomica.rotation.SingleDumbellRattle
main(String[]) - Static method in class etomica.rotation.SingleDumbellShake
main(String[]) - Static method in class etomica.rotation.SingleWater
main(String[]) - Static method in class etomica.rotation.SingleWaterMatrix
main(String[]) - Static method in class etomica.rotation.SingleWaterRattle
main(String[]) - Static method in class etomica.rotation.SingleWaterShake
main(String[]) - Static method in class etomica.rotation.WaterBox
main(String[]) - Static method in class etomica.rotation.WaterDroplet
main(String[]) - Static method in class etomica.rotation.WaterDropletMatrix
main(String[]) - Static method in class etomica.rotation.WaterDropletRattle
main(String[]) - Static method in class etomica.rotation.WaterDropletShake
main(String[]) - Static method in class etomica.rotation.WaterTrimer
main(String[]) - Static method in class etomica.rotation.WaterTrimerRattle
main(String[]) - Static method in class etomica.rotation.WaterTrimerShake
main(String[]) - Static method in class etomica.simulation.prototypes.ChainHSMD3D
main(String[]) - Static method in class etomica.simulation.prototypes.HSMD2D: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.simulation.prototypes.HSMD2D_noNbr: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.simulation.prototypes.HSMD3D: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.simulation.prototypes.HSMD3DNoNbr
main(String[]) - Static method in class etomica.simulation.prototypes.LjMd3D
main(String[]) - Static method in class etomica.simulation.prototypes.SoftSphere3d
main(String[]) - Static method in class etomica.simulation.prototypes.SWMD3D: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.space3d.RotationTensor3D: Method to test rotation tensor.
main(String[]) - Static method in class etomica.spin.Heisenberg
main(String[]) - Static method in class etomica.statmech.HardSphere
main(String[]) - Static method in class etomica.statmech.HardSphereSolid
main(String[]) - Static method in class etomica.statmech.LennardJones
main(String[]) - Static method in class etomica.surfacetension.FitTanh
main(String[]) - Static method in class etomica.surfacetension.LJMC
main(String[]) - Static method in class etomica.tests.TestHSMD3D: Demonstrates how this class is implemented.
main(String[]) - Static method in class etomica.tests.TestLJMC3D
main(String[]) - Static method in class etomica.tests.TestSWChain
main(String[]) - Static method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
main(String[]) - Static method in class etomica.thermointegration.LjMc3D
main(String[]) - Static method in class etomica.threaded.atom.LJMD3DThreaded
main(String[]) - Static method in class etomica.threaded.atom.LJMD3DThreadedforCluster
main(String[]) - Static method in class etomica.threaded.domain.LJMD3DThreaded
main(String[]) - Static method in class etomica.threaded.domain.LJMD3DThreadedforCluster
main(String[]) - Static method in class etomica.threaded.domain.MEAMMd3DThreaded
main(String[]) - Static method in class etomica.threaded.domain.MEAMMd3DThreadedforCluster
main(String[]) - Static method in class etomica.threads.AtomDecompositionMD
main(String[]) - Static method in class etomica.units.Tester
main(String[]) - Static method in class etomica.units.UnitFilter
main(String[]) - Method in class etomica.units.UnitGraphics
main(String[]) - Static method in class etomica.util.Constants
main(String[]) - Static method in class etomica.util.FastFourierTransform
main(String[]) - Static method in class etomica.util.Grabber
main(String[]) - Static method in class etomica.util.MersenneTwister: Tests the code.
main(String[]) - Static method in class etomica.util.MersenneTwisterFast: Tests the code.
main(String[]) - Static method in class etomica.util.numerical.AkimaSpline
main(String[]) - Static method in class etomica.util.numerical.AkimaSplineSmootherApp
main(String[]) - Static method in class etomica.util.numerical.AkimaSplineSmootherDyApp
main(String[]) - Static method in class etomica.util.numerical.AkimaSplineSmootherMain
main(String[]) - Static method in class etomica.util.numerical.B9Optimizer
main(String[]) - Static method in class etomica.util.numerical.LinearFit
main(String[]) - Static method in class etomica.util.numerical.NonLinearCurveDiffFitting
main(String[]) - Static method in class etomica.util.numerical.NonLinearCurveFitting
main(String[]) - Static method in class etomica.util.numerical.PadeApproximation
main(String[]) - Static method in class etomica.util.numerical.PolynomialFit
main(String[]) - Static method in class etomica.util.numerical.VirialOptimizer
main(String[]) - Static method in class etomica.util.OdeSolver: Test of integration algorithm.
main(String[]) - Static method in class etomica.util.RandomNumberGeneratorUnix
main(String[]) - Static method in class etomica.util.ReadParameters
main(String[]) - Static method in class etomica.util.ScientificFormat
main(String[]) - Static method in class etomica.util.Strings
main(String[]) - Static method in class etomica.veos.bigdecimal.EulerPhi: Test program.
main(String[]) - Static method in class etomica.veos.bigdecimal.Ifactor: Test program.
main(String[]) - Static method in class etomica.veos.bigdecimal.PartitionsP: Test program.
main(String[]) - Static method in class etomica.veos.bigdecimal.Prime: Test program.
main(String[]) - Static method in class etomica.veos.bigdecimal.Wigner3j: Test programs.
main(String[]) - Static method in class etomica.veos.bigdecimal.Wigner3jGUI: Main entry point.
main(String[]) - Static method in class etomica.veos.BigValue
main(String[]) - Static method in class etomica.veos.MyBigDecimal
main(String[]) - Static method in class etomica.veos.QSeries
main(String[]) - Static method in class etomica.veos.Ushcats
main(String[]) - Static method in class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
main(String[]) - Static method in class etomica.virial.B2Ionic
main(String[]) - Static method in class etomica.virial.B3ForSphericallySymmetricU
main(String[]) - Static method in class etomica.virial.B3LJ
main(String[]) - Static method in class etomica.virial.B3NonAddForSphericallySymmetricU
main(String[]) - Static method in class etomica.virial.B4FFTLJ
main(String[]) - Static method in class etomica.virial.B5FFTLJ
main(String[]) - Static method in class etomica.virial.B6FFTLJ
main(String[]) - Static method in class etomica.virial.BnHNCLJ
main(String[]) - Static method in class etomica.virial.BnHSIonic
main(String[]) - Static method in class etomica.virial.BnIETP2Spherical
main(String[]) - Static method in class etomica.virial.BnJHBVArgon_Analytic
main(String[]) - Static method in class etomica.virial.BnPY_1QC_Helium
main(String[]) - Static method in class etomica.virial.BnPYCHe
main(String[]) - Static method in class etomica.virial.BnPYHardSphere
main(String[]) - Static method in class etomica.virial.BnPYLJ
main(String[]) - Static method in class etomica.virial.BnSCALJ
main(String[]) - Static method in class etomica.virial.CalcFFT
main(String[]) - Static method in class etomica.virial.cluster.ClusterDiagram
main(String[]) - Static method in class etomica.virial.cluster.ClusterGenerator: Demonstrates how to use this class.
main(String[]) - Static method in class etomica.virial.cluster.ClusterOperations
main(String[]) - Static method in class etomica.virial.cluster.DCF
main(String[]) - Static method in class etomica.virial.cluster.ExternalVirialDiagrams
main(String[]) - Static method in class etomica.virial.cluster.MayerIonicDiagram1qbond
main(String[]) - Static method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
main(String[]) - Static method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
main(String[]) - Static method in class etomica.virial.cluster.PermutationIterator
main(String[]) - Static method in class etomica.virial.cluster.Standard
main(String[]) - Static method in class etomica.virial.cluster.VirialDiagrams
main(String[]) - Static method in class etomica.virial.cluster.VirialDiagramsMix
main(String[]) - Static method in class etomica.virial.cluster.VirialDiagramsMix2
main(String[]) - Static method in class etomica.virial.cluster.VirialDiagramsPT
main(String[]) - Static method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
main(String[]) - Static method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
main(String[]) - Static method in class etomica.virial.ClusterBonds
main(String[]) - Static method in class etomica.virial.ClusterChainHS
main(String[]) - Static method in class etomica.virial.ClusterSinglyConnected
main(String[]) - Static method in class etomica.virial.ClusterWheatleyPartitionScreening
main(String[]) - Static method in class etomica.virial.GUI.ApplicationMixtureBuilder
main(String[]) - Static method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
main(String[]) - Static method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
main(String[]) - Static method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
main(String[]) - Static method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
main(String[]) - Static method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
main(String[]) - Static method in class etomica.virial.GUI.models.ViewSpeciesSelection
main(String[]) - Static method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
main(String[]) - Static method in class etomica.virial.GUI.views.ViewSpeciesSelection
main(String[]) - Static method in class etomica.virial.HNCGenerator
main(String[]) - Static method in class etomica.virial.IsFFT
main(String[]) - Static method in class etomica.virial.MCMoveClusterAtomHSRing
main(String[]) - Static method in class etomica.virial.MCMoveClusterRingRegrowOrientation
main(String[]) - Static method in class etomica.virial.PotentialNonAdditive
main(String[]) - Static method in class etomica.virial.PYGenerator
main(String[]) - Static method in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
main(String[]) - Static method in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr
main(String[]) - Static method in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt
main(String[]) - Static method in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt
main(String[]) - Static method in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt
main(String[]) - Static method in class etomica.virial.simulations.FourAssociationSitesFluid2Pt
main(String[]) - Static method in class etomica.virial.simulations.LJTSRefLJ
main(String[]) - Static method in class etomica.virial.simulations.ReeHooverMC
main(String[]) - Static method in class etomica.virial.simulations.SimulationVirialMultiOverlap
main(String[]) - Static method in class etomica.virial.simulations.SimulationVirialUmbrella
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid2
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid4Points
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt
main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluidGraph
main(String[]) - Static method in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
main(String[]) - Static method in class etomica.virial.simulations.Virial2CLJQ
main(String[]) - Static method in class etomica.virial.simulations.Virial7SiteRigidSF6
main(String[]) - Static method in class etomica.virial.simulations.VirialAceticAcid
main(String[]) - Static method in class etomica.virial.simulations.VirialAceticAcidFlex
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkane
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneFull
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix2
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix2_Kong
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix_Kong
main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneSKS
main(String[]) - Static method in class etomica.virial.simulations.VirialAnthracene464
main(String[]) - Static method in class etomica.virial.simulations.VirialAnthracene545
main(String[]) - Static method in class etomica.virial.simulations.VirialAnthraceneTraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialAssociatingFluid
main(String[]) - Static method in class etomica.virial.simulations.VirialAssociatingFluid4points
main(String[]) - Static method in class etomica.virial.simulations.VirialB3C1HSDipole
main(String[]) - Static method in class etomica.virial.simulations.VirialB3C2HSDipole
main(String[]) - Static method in class etomica.virial.simulations.VirialCH4AlkaneEHMix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2AlkaneEHMix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2AlkaneUAMix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2anthracene464
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2anthracene545
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2CH4Mix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2CH4UAMix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2H2OGCPM
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2H2OGCPMX
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2H2OSC
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2LJQ
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2N2Mix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2PI
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2SKSMix
main(String[]) - Static method in class etomica.virial.simulations.VirialCO2TraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialCPSHeliumNonAdditive
main(String[]) - Static method in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
main(String[]) - Static method in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
main(String[]) - Static method in class etomica.virial.simulations.VirialEmulNonAdditive
main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldOverlapRho
main(String[]) - Static method in class etomica.virial.simulations.VirialGCPM
main(String[]) - Static method in class etomica.virial.simulations.VirialGCPMGraphic
main(String[]) - Static method in class etomica.virial.simulations.VirialH2O
main(String[]) - Static method in class etomica.virial.simulations.VirialH2PI
main(String[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
main(String[]) - Static method in class etomica.virial.simulations.VirialH2PISimple
main(String[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
main(String[]) - Static method in class etomica.virial.simulations.VirialH2PYCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialHardAssociationCone
main(String[]) - Static method in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites
main(String[]) - Static method in class etomica.virial.simulations.VirialHeNonAdditive
main(String[]) - Static method in class etomica.virial.simulations.VirialHeNonAdditiveWheatley
main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJS
main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJSPYCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJSTempDeriv
main(String[]) - Static method in class etomica.virial.simulations.VirialHePI
main(String[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialHePIGraphic
main(String[]) - Static method in class etomica.virial.simulations.VirialHePIXC
main(String[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
main(String[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
main(String[]) - Static method in class etomica.virial.simulations.VirialHePYCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialHeSC
main(String[]) - Static method in class etomica.virial.simulations.VirialHS
main(String[]) - Static method in class etomica.virial.simulations.VirialHSBinMultiThreaded
main(String[]) - Static method in class etomica.virial.simulations.VirialHSOrC
main(String[]) - Static method in class etomica.virial.simulations.VirialLJ
main(String[]) - Static method in class etomica.virial.simulations.VirialLJBridge
main(String[]) - Static method in class etomica.virial.simulations.VirialLJCHNCCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialLJMultiOverlap
main(String[]) - Static method in class etomica.virial.simulations.VirialLJOrC
main(String[]) - Static method in class etomica.virial.simulations.VirialLJOrICPYC
main(String[]) - Static method in class etomica.virial.simulations.VirialLJPYCorrection
main(String[]) - Static method in class etomica.virial.simulations.VirialLJSeries
main(String[]) - Static method in class etomica.virial.simulations.VirialMethaneEH
main(String[]) - Static method in class etomica.virial.simulations.VirialN2
main(String[]) - Static method in class etomica.virial.simulations.VirialN2AlkaneEHMix
main(String[]) - Static method in class etomica.virial.simulations.VirialN2AlkaneUAMix
main(String[]) - Static method in class etomica.virial.simulations.VirialN2AlkaneUARigid
main(String[]) - Static method in class etomica.virial.simulations.VirialN2CH4Mix
main(String[]) - Static method in class etomica.virial.simulations.VirialN2CH4UAMix
main(String[]) - Static method in class etomica.virial.simulations.VirialN2PI
main(String[]) - Static method in class etomica.virial.simulations.VirialN2TraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialNaphthaleneTraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialO2
main(String[]) - Static method in class etomica.virial.simulations.VirialO2PI
main(String[]) - Static method in class etomica.virial.simulations.VirialPh464
main(String[]) - Static method in class etomica.virial.simulations.VirialPh545
main(String[]) - Static method in class etomica.virial.simulations.VirialPhenanthreneTraPPE
main(String[]) - Static method in class etomica.virial.simulations.VirialPolyhedra
main(String[]) - Static method in class etomica.virial.simulations.VirialPolyhedra2
main(String[]) - Static method in class etomica.virial.simulations.VirialRowleyAlcohol
main(String[]) - Static method in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix
main(String[]) - Static method in class etomica.virial.simulations.VirialSQWBinMultiRecalcW
main(String[]) - Static method in class etomica.virial.simulations.VirialSQWBinMultiThreaded
main(String[]) - Static method in class etomica.virial.simulations.VirialSQWRecalcSmallMem
main(String[]) - Static method in class etomica.virial.simulations.VirialSW
main(String[]) - Static method in class etomica.virial.simulations.VirialSwsPT
main(String[]) - Static method in class etomica.virial.simulations.VirialSWWE
main(String[]) - Static method in class etomica.virial.simulations.VirialTraPPEAlcohol
main(String[]) - Static method in class etomica.virial.simulations.VirialWaterOverlap
main(String[]) - Static method in class etomica.yukawa.TestHC2YukawaMC3D
main(String[]) - Static method in class etomica.yukawa.TestYukawaMC3D
main(String[]) - Static method in class etomica.yukawa.TestYukawaMD3D
main(String[]) - Static method in class etomica.zeolite.DataCutter
main(String[]) - Static method in class etomica.zeolite.DeviceButtonSingle: Method to demonstrate and test the use of this class.
main(String[]) - Static method in class etomica.zeolite.Zeolite
main(String[]) - Static method in class etomica.zeolite.ZeoliteSimulation: Demonstrates how this class is implemented.
Main.AbstractOptionHandler - Class in etomica.graph.view.rasterizer: This abstract implementation of the OptionHandler interface throws an exception if the number of arguments passed to the handleOption method does not match the number of expected optionValues.
Main.ColorOptionHandler - Class in etomica.graph.view.rasterizer: Base class for options which expect a Color optionValue.
Main.FloatOptionHandler - Class in etomica.graph.view.rasterizer: Base class for options which expect the single optionValue to be a float.
Main.NoValueOptionHandler - Class in etomica.graph.view.rasterizer: Base class for options with no option value (i.e., the presence of the option means something in itself.
Main.OptionHandler - Interface in etomica.graph.view.rasterizer: Interface for handling one command line option
Main.RectangleOptionHandler - Class in etomica.graph.view.rasterizer: Base class for options which expect a Rectangle optionValue.
Main.SingleValueOptionHandler - Class in etomica.graph.view.rasterizer: Base class for options with a single option value.
Main.TimeOptionHandler - Class in etomica.graph.view.rasterizer: Base class for options which expect the single optionValue to be a time value.
main1(String[]) - Static method in class etomica.models.co2.P2CO2Hellmann
main1(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
main2(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
main2(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
main2(String[]) - Static method in class etomica.models.co2.PNCO2GCPM
main2(String[]) - Static method in class etomica.models.co2.PNGCPM
main2(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
main2DGrid(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley: Writes a x-y grid of energies
main3(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
mainCO2(String[]) - Static method in class etomica.models.co2.PNGCPM
mainQ(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
mainTestU(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
makeAdjacentPairIterator() - Static method in class etomica.atom.iterator.ApiBuilder: Pair iterator that constructs pairs from the childlist atoms of a basis, each with the atom adjacent to it in the list.
makeAgent(IAtom, IBox) - Method in class etomica.association.AssociationManager
makeAgent(IMolecule) - Method in class etomica.association.AssociationManagerMolecule
makeAgent(IAtom, IBox) - Method in class etomica.association.ColorSchemeSmer
makeAgent(IAtom, IBox) - Method in class etomica.association.MCMoveVolumeAssociated
makeAgent(IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
makeAgent(IAtom, IBox) - Method in interface etomica.atom.AtomLeafAgentManager.AgentSource: Returns an agent for the given Atom.
makeAgent(IAtomType) - Method in interface etomica.atom.AtomTypeAgentManager.AgentSource: Returns an agent for the given AtomType.
makeAgent(IAtomType) - Method in class etomica.atom.DiameterHashByType
makeAgent(IMolecule) - Method in interface etomica.atom.MoleculeAgentManager.MoleculeAgentSource: Returns an agent for the given Atom.
makeAgent(ISpecies) - Method in interface etomica.atom.SpeciesAgentManager.AgentSource: Returns an agent for the given AtomType.
makeAgent(IBox) - Method in interface etomica.box.BoxAgentManager.BoxAgentSource
makeAgent(IBox) - Method in class etomica.box.BoxAgentSourceAtomManager
makeAgent(IBox) - Method in class etomica.box.BoxAgentSourceMoleculeManager
makeAgent(IAtom, IBox) - Method in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
makeAgent(IAtom, IBox) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
makeAgent(IMolecule) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
makeAgent(IAtom, IBox) - Method in class etomica.dimer.IntegratorDimerMin
makeAgent(IAtom, IBox) - Method in class etomica.dimer.IntegratorDimerRT
makeAgent(IAtom, IBox) - Method in class etomica.dimer.IntegratorEnergyMap
makeAgent(IAtom, IBox) - Method in class etomica.graphics.BondListener
makeAgent(IAtomType) - Method in class etomica.graphics.ColorSchemeByType
makeAgent(IAtom, IBox) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
makeAgent(IAtom, IBox) - Method in class etomica.graphics.ColorSchemeRandom
makeAgent(IMolecule) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
makeAgent(IAtom, IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: AgentSource methods
makeAgent(IAtom, IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorConNVT
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorGear4
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorHard: Produces the Agent for this integrator.
makeAgent(IAtomType) - Method in class etomica.integrator.IntegratorHard
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorMD.VectorSource
makeAgent(IMolecule) - Method in class etomica.integrator.IntegratorRigidIterative
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorRigidIterative
makeAgent(ISpecies) - Method in class etomica.integrator.IntegratorRigidIterative
makeAgent(IMolecule) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
makeAgent(ISpecies) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorVelocityVerlet
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorVelocityVerletShake
makeAgent(ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
makeAgent(IAtom, IBox) - Method in class etomica.integrator.IntegratorVerlet
makeAgent(IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedU
makeAgent(IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedVirial
makeAgent(IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedVirialV
makeAgent(IAtom, IBox) - Method in class etomica.mappedvirial.MeterMeanForce
makeAgent(IAtom, IBox) - Method in class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
makeAgent(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
makeAgent(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
makeAgent(IAtom, IBox) - Method in class etomica.models.water.ChargeAgentSourceTIP4PWater
makeAgent(IAtom, IBox) - Method in class etomica.modules.catalysis.InteractionTracker
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim: Implementation of AtomAgentManager.AgentSource interface.
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
makeAgent(IAtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim: Implementation of AtomAgentManager.AgentSource interface.
makeAgent(IAtom, IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
makeAgent(IBox) - Method in class etomica.modules.colloid.NeighborListManagerColloid.NeighborListAgentSourceColloid
makeAgent(IAtom, IBox) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
makeAgent(IAtom, IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
makeAgent(IAtom, IBox) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium: Implementation of Atom.AgentSource interface.
makeAgent(IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
makeAgent(IAtom, IBox) - Method in class etomica.modules.rosmosis.P1Tether
makeAgent(IMolecule) - Method in class etomica.modules.sam.CriterionTether3
makeAgent(IBox) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
makeAgent(IBox) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
makeAgent(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Returns the cell containing the given atom.
makeAgent(IAtom, IBox) - Method in class etomica.nbr.cell.NeighborCellManager: Returns the cell containing the given atom.
makeAgent(IAtom, IBox) - Method in class etomica.nbr.CriterionPositionWall
makeAgent(IAtom, IBox) - Method in class etomica.nbr.CriterionSimple
makeAgent(IBox) - Method in class etomica.nbr.list.BoxAgentSourceCellManagerList
makeAgent(IBox) - Method in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
makeAgent(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
makeAgent(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
makeAgent(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
makeAgent(IBox) - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular
makeAgent(IBox) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
makeAgent(IAtom, IBox) - Method in class etomica.nbr.list.NeighborCellManagerList
makeAgent(IAtom, IBox) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
makeAgent(IAtom, IBox) - Method in class etomica.nbr.list.NeighborListManager
makeAgent(IBox) - Method in class etomica.nbr.list.NeighborListManagerSlanty.NeighborListSlantyAgentSource
makeAgent(IBox) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
makeAgent(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
makeAgent(ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
makeAgent(IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
makeAgent(ISpecies) - Method in class etomica.nbr.PotentialMasterNbr
makeAgent(IAtom, IBox) - Method in class etomica.nbr.site.NeighborSiteManager
makeAgent(IBox) - Method in class etomica.nbr.site.PotentialMasterSite.BoxAgentSiteSource
makeAgent(IAtom, IBox) - Method in class etomica.normalmode.CoordinateDefinition.SiteSource
makeAgent(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
makeAgent(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
makeAgent(IAtom, IBox) - Method in class etomica.normalmode.HSNPT.ActionSummer
makeAgent(IAtom, IBox) - Method in class etomica.normalmode.MeterDADB
makeAgent(IAtom, IBox) - Method in class etomica.normalmode.MeterSolidProps
makeAgent(IAtom, IBox) - Method in class etomica.normalmode.MeterSolidPropsLJ
makeAgent(IAtom, IBox) - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
makeAgent(IMolecule) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
makeAgent(IAtom, IBox) - Method in class etomica.potential.P2HardBondedList
makeAgent(IBox) - Method in class etomica.potential.P2SquareWellRobust
makeAgent(IAtom, IBox) - Method in class etomica.potential.P2SquareWellRobust
makeAgent(IAtomType) - Method in class etomica.potential.PotentialMasterMonatomic
makeAgent(IMolecule) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
makeAgent(IAtom, IBox) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
makeAgent(ISpecies) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
makeAgent(IAtom, IBox) - Method in class etomica.surfacetension.SurfaceTensionMapped
makeAgent(IBox) - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
makeAgent(IBox) - Method in class etomica.threaded.domain.PotentialMasterListThreaded.NeighborListAgentSourceThreaded
makeAgent(IAtom, IBox) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
makeAgent(IAtom, IBox) - Method in class etomica.util.numerical.CalcGradientDifferentiable
makeAndDisplayFrame() - Method in class etomica.graphics.SimulationGraphic
makeAndDisplayFrame(String) - Method in class etomica.graphics.SimulationGraphic
makeAndDisplayFrame(JPanel, String) - Static method in class etomica.graphics.SimulationGraphic
makeAndDisplayFrame(JPanel) - Static method in class etomica.graphics.SimulationGraphic
makeArrayD(int) - Method in interface etomica.space.ISpace: Returns an array of dimension D, with each element equal to the given value.
makeArrayD(double) - Method in interface etomica.space.ISpace: Returns an array of dimension D, with each element equal to the given value.
makeArrayD(int) - Method in class etomica.space.Space
makeArrayD(double) - Method in class etomica.space.Space
makeArrayD(int) - Method in class etomica.space1d.Space1D
makeArrayD(double) - Method in class etomica.space1d.Space1D
makeArrayD(int) - Method in class etomica.space2d.Space2D
makeArrayD(double) - Method in class etomica.space2d.Space2D
makeArrayD(int) - Method in class etomica.space3d.Space3D
makeArrayD(double) - Method in class etomica.space3d.Space3D
makeAtomTypes(IElement[]) - Static method in class etomica.species.SpeciesSpheresCustom
makeAtomTypes(IElement[]) - Static method in class etomica.species.SpeciesSpheresHetero
makeAxilrodTeller() - Method in class etomica.models.co2.PNCO2GCPM
makeAxilrodTeller() - Method in class etomica.models.co2.PNGCPM
makeBigValue(double) - Method in class etomica.veos.Ushcats
makeBigValue(IBigValue) - Method in class etomica.veos.Ushcats
makeBond(IAtomList, Object) - Method in interface etomica.graphics.BondManager: Creates a bond object for the given pair with type determined by the bondType object.
makeBond(IAtomList, Object) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Add a bond to the graphical display between the given pairs.
makeBox(ISpace, ClusterWeight) - Method in class etomica.virial.simulations.SimulationVirialOverlap2.BoxClusterFactory
makeCachedPairPolarization() - Method in class etomica.models.co2.PNGCPM
makeCopy() - Method in interface etomica.virial.ClusterAbstract: Returns another instance of an identical cluster (shallow copy).
makeCopy() - Method in class etomica.virial.ClusterChainHS
makeCopy() - Method in class etomica.virial.ClusterChainSoft
makeCopy() - Method in class etomica.virial.ClusterCoupledAtomFlipped
makeCopy() - Method in class etomica.virial.ClusterCoupledFlipped
makeCopy() - Method in class etomica.virial.ClusterCoupledFlippedPartial
makeCopy() - Method in class etomica.virial.ClusterDifference
makeCopy() - Method in class etomica.virial.ClusterExchange
makeCopy() - Method in class etomica.virial.ClusterSinglyConnected
makeCopy() - Method in class etomica.virial.ClusterSum
makeCopy() - Method in class etomica.virial.ClusterSumAssociation
makeCopy() - Method in class etomica.virial.ClusterSumEF
makeCopy() - Method in class etomica.virial.ClusterSumHS
makeCopy() - Method in class etomica.virial.ClusterSumIC
makeCopy() - Method in class etomica.virial.ClusterSumMultibody
makeCopy() - Method in class etomica.virial.ClusterSumMultibodyShell
makeCopy() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
makeCopy() - Method in class etomica.virial.ClusterSumPolarizable
makeCopy() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
makeCopy() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
makeCopy() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
makeCopy() - Method in class etomica.virial.ClusterSumShell
makeCopy() - Method in class etomica.virial.ClusterTree
makeCopy() - Method in class etomica.virial.ClusterTreeEF
makeCopy() - Method in class etomica.virial.ClusterWeightAbs
makeCopy() - Method in class etomica.virial.ClusterWeightSumWall
makeCopy() - Method in class etomica.virial.ClusterWeightUmbrella
makeCopy() - Method in class etomica.virial.ClusterWheatleyExtendSW
makeCopy() - Method in class etomica.virial.ClusterWheatleyHS
makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibody
makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyBD
makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyMix
makeCopy() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
makeCopy() - Method in class etomica.virial.ClusterWheatleySoft
makeCopy() - Method in class etomica.virial.ClusterWheatleySoftBD
makeCopy() - Method in class etomica.virial.ClusterWheatleySoftBDMix
makeCopy() - Method in class etomica.virial.ClusterWheatleySoftMix
makeData() - Method in interface etomica.data.IDataInfo: Returns a Data object appropriate for this DataInfo instance.
makeData() - Method in class etomica.data.types.DataDouble.DataInfoDouble
makeData() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
makeData() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
makeData() - Method in class etomica.data.types.DataFunction.DataInfoFunction
makeData() - Method in class etomica.data.types.DataGroup.DataInfoGroup
makeData() - Method in class etomica.data.types.DataTable.DataInfoTable
makeData(int, int) - Static method in class etomica.data.types.DataTable
makeData() - Method in class etomica.data.types.DataTensor.DataInfoTensor
makeData() - Method in class etomica.data.types.DataVector.DataInfoVector
MakeData - Class in etomica.models.oneDHardRods
MakeData(int, double) - Constructor for class etomica.models.oneDHardRods.MakeData
makeData(int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
makeDataInfo() - Method in class etomica.data.DataInfoFactory: Creates a new DataInfo object using the information held by this factory.
makeDataInfo() - Method in interface etomica.data.IEtomicaDataInfoFactory: Creates a new DataInfo object using the information held by this factory.
makeDataInfo() - Method in class etomica.data.types.DataDouble.DataInfoDoubleFactory
makeDataInfo() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
makeDataInfo() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
makeDataInfo() - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory
makeDataInfo() - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
makeDataInfo() - Method in class etomica.data.types.DataTable.DataInfoTableFactory
makeDataInfo() - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory
makeDataInfo() - Method in class etomica.data.types.DataVector.DataInfoVectorFactory
makeDataSink() - Method in class etomica.data.DataSet
makeDataSink(int) - Method in interface etomica.data.DataSplitter.IDataSinkFactory
makeDipole() - Static method in class etomica.rotation.SingleDipole
makeDropShape() - Method in class etomica.modules.droplet.DropletAtomic
makeDWPlot - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
makeF(Potential2Spherical, double) - Static method in class etomica.virial.CalcFFT
makeFccVectors(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
makeFullStar() - Method in class etomica.virial.cluster.ClusterDiagram: Turns this cluster into a full star -- each point in the cluster is connected to every other point in the cluster.
makeGraph(long) - Static method in class etomica.graph.util.GraphNumber
makeGraph(long, byte) - Static method in class etomica.graph.util.GraphNumber
makeGraphicsPanel() - Method in class etomica.modules.clustergenerator.MyApplet
makeGraphList() - Static method in class etomica.virial.cluster.MayerIonicDiagram1qbond
makeGraphList() - Static method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
makeGraphList() - Static method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
makeGraphList() - Static method in class etomica.virial.cluster.VirialDiagrams
makeGraphList() - Method in class etomica.virial.cluster.VirialDiagramsMix
makeGraphList() - Method in class etomica.virial.cluster.VirialDiagramsMix2
makeGraphList() - Static method in class etomica.virial.cluster.VirialDiagramsPT
makeGraphList() - Static method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
makeGraphList() - Static method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
makeHcpVectors(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
makeInputFile(IVectorMutable, IVectorMutable) - Method in class etomica.potential.P2QChem
makeInputFile(IMoleculeList) - Method in class etomica.potential.PotentialEmul
makeIntergroupTypeIterator(IAtomType[]) - Static method in class etomica.atom.iterator.ApiBuilder: Returns an intergroup iterator that filters the iterates so that only those having the given type instances are returned.
makeInterspeciesPairIterator(ISpecies[]) - Method in class etomica.atom.iterator.IteratorFactory: creates a pair iterator which loops over all pairs in a neighbor list between two groups
makeIntraspeciesPairIterator(ISpecies) - Method in class etomica.atom.iterator.IteratorFactory: creates a pair iterator which loops over all pairs in a neighbor list within one group
makeIterator() - Method in class etomica.atom.AtomLeafAgentManager: Returns an iterator that returns each non-null agent
makeIterator() - Method in class etomica.atom.AtomTypeAgentManager: Returns an iterator that returns each non-null agent
makeIterator() - Method in class etomica.atom.MoleculeAgentManager: Returns an iterator that returns each non-null agent
makeIterator() - Method in class etomica.atom.SpeciesAgentManager: Returns an iterator that returns each non-null agent
makeIterator() - Method in class etomica.box.BoxAgentManager: Returns an iterator that returns each non-null agent
makeLeafAtom(IAtomType) - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
makeLeafAtom(IAtomType) - Method in class etomica.paracetamol.SpeciesParacetamol
makeLeafAtom() - Method in class etomica.species.SpeciesPolyhedron
makeLeafAtom() - Method in class etomica.species.SpeciesSpheres
makeLeafAtom(IAtomType) - Method in class etomica.species.SpeciesSpheresCustom
makeLeafAtom(IAtomType) - Method in class etomica.species.SpeciesSpheresHetero
makeLeafAtom() - Method in class etomica.species.SpeciesSpheresMono
makeLeafAtom() - Method in class etomica.species.SpeciesSpheresRotating
makeLeafAtom() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
makeLeafAtom(IAtomType) - Method in class etomica.virial.SpeciesAlkaneEH
makeLrc - Variable in class etomica.potential.P2SoftSphericalTruncated
makeLrcPotential(IAtomType[]) - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the zero-body potential that evaluates the contribution to the energy and its derivatives from pairs that are separated by a distance exceeding the truncation radius.
makeLrcPotential(IAtomType[]) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted: Returns null because the shift can't be corrected.
makeLrcPotential(IAtomType[]) - Method in class etomica.potential.P2SoftTruncated: Returns the zero-body potential that evaluates the contribution to the energy and its derivatives from pairs that are separated by a distance exceeding the truncation radius.
makeLrcPotential(IAtomType[]) - Method in interface etomica.potential.PotentialTruncated: Returns a class that calculates the long-range contribution to the potential that becomes neglected by the truncation.
makeMCMoveListener() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
makeMCMoveListener() - Method in class etomica.nbr.cell.NeighborCellManager
makeMCMoveSwap(IntegratorBox, IntegratorBox, ISpace) - Method in interface etomica.integrator.IntegratorPT.MCMoveSwapFactory
makeMCMoveSwap(IntegratorBox, IntegratorBox, ISpace) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory
makeMCMoveSwap(IntegratorBox, IntegratorBox, ISpace) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster.SwapFactory
makeMolecule() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
makeMolecule() - Method in class etomica.AlkaneEH.SpeciesMethane
makeMolecule() - Method in interface etomica.api.ISpecies: Builds and returns the IMolecule of this ISpecies.
makeMolecule() - Method in class etomica.models.nitrogen.SpeciesN2
makeMolecule() - Method in class etomica.models.nitrogen.SpeciesN2B
makeMolecule() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
makeMolecule() - Method in class etomica.models.OPLS.SpeciesAceticAcid
makeMolecule() - Method in class etomica.models.rowley.SpeciesEthanol
makeMolecule() - Method in class etomica.models.rowley.SpeciesMethanol
makeMolecule() - Method in class etomica.models.traPPE.SpeciesMethanol
makeMolecule() - Method in class etomica.models.water.SpeciesWater3P
makeMolecule() - Method in class etomica.models.water.SpeciesWater3POriented
makeMolecule() - Method in class etomica.models.water.SpeciesWater4P
makeMolecule() - Method in class etomica.models.water.SpeciesWater4PCOM
makeMolecule() - Method in class etomica.models.water.SpeciesWater4POriented
makeMolecule() - Method in class etomica.normalmode.SpeciesHSDimer
makeMolecule() - Method in class etomica.paracetamol.SpeciesParacetamol
makeMolecule() - Method in class etomica.species.SpeciesSpheres: Constructs a new group.
makeMolecule() - Method in class etomica.species.SpeciesSpheresCustom: Constructs a new group containing a block of atoms for each sub-type.
makeMolecule() - Method in class etomica.species.SpeciesSpheresHetero: Constructs a new group containing a block of atoms for each sub-type.
makeMolecule() - Method in class etomica.species.SpeciesSpheresMono: Constructs a new group.
makeMolecule() - Method in class etomica.species.SpeciesSpheresRotatingMolecule: Constructs a new group.
makeMolecule() - Method in class etomica.virial.Species7SiteRigidSF6
makeMolecule() - Method in class etomica.virial.SpeciesAlkane
makeMolecule() - Method in class etomica.virial.SpeciesAlkaneEH
makeMolecule() - Method in class etomica.virial.SpeciesAnthracene3site464
makeMolecule() - Method in class etomica.virial.SpeciesAnthracene3site545
makeMolecule() - Method in class etomica.virial.SpeciesMethane
makeMolecule() - Method in class etomica.virial.SpeciesPh3site464
makeMolecule() - Method in class etomica.virial.SpeciesPh3site545
makeMolecule() - Method in class etomica.virial.SpeciesTraPPEAnthracene
makeMolecule() - Method in class etomica.virial.SpeciesTraPPECO2
makeMolecule() - Method in class etomica.virial.SpeciesTraPPENaphthalene
makeMolecule() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
makeMoleculeIterator(ISpecies[]) - Method in class etomica.atom.iterator.IteratorFactory: Selects an appropriate iterator for the given species array.
makeNB(int) - Method in class etomica.virial.PotentialNonAdditive
makeNominalMoment(ISpace) - Static method in class etomica.species.SpeciesSpheresRotatingMolecule
makeNonAdjacentPairIterator() - Static method in class etomica.atom.iterator.ApiBuilder: Pair iterator that constructs pairs from the childlist atoms of a basis, each with all atoms that are not adjacent to it in the list.
makeNonAdjacentPairIterator(int) - Static method in class etomica.atom.iterator.ApiBuilder
makeOrientation() - Method in interface etomica.space.ISpace: Constructs and returns a new Orientation appropriate to the space.
makeOrientation() - Method in class etomica.space.Space
makeOrientation() - Method in class etomica.space1d.Space1D
makeOrientation() - Method in class etomica.space2d.Space2D
makeOrientation() - Method in class etomica.space3d.Space3D
makeP0() - Method in class etomica.potential.P2ReactionFieldDipole: Returns a 0-body potential that should be added along with this potential.
makeP0() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated: Returns a 0-body potential that should be added along with this potential.
makeP1IntraSimple(IPotentialMaster, Potential2, Potential2) - Static method in class etomica.potential.P1IntraSimple
makeP2EwaldReal() - Method in class etomica.potential.EwaldSummation
makePairPotentialsUnlike(int, int) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
makeParameters(char[], byte) - Static method in class etomica.graph.operations.MulFlexible.MulFlexibleParameters: Parameters that specify that the resulting product should include graphs containing up to nFieldNodes field nodes and that nodes of a color included in flexColors never be superimposed unless one of the nodes is unbonded.
makeParametersOnlyRootPt(char[], byte) - Static method in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
makeParametersWithNodes(char[], byte, byte, byte) - Static method in class etomica.graph.operations.MulFlexible.MulFlexibleParameters: Parameters that specify that the resulting product should include graphs containing up to nFieldNodes field nodes and that node1ID from the first graph and node2ID from the second graph should be superimposed (if possible).
makePotentialGroup(int) - Method in interface etomica.api.IPotentialMaster: Returns an nBody PotentialGroup appropriate for this type of PotentialMaster.
makePotentialGroup(int) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
makePotentialGroup(int) - Method in class etomica.nbr.PotentialMasterHybrid
makePotentialGroup(int) - Method in class etomica.nbr.PotentialMasterNbr
makePotentialGroup(int) - Method in class etomica.potential.PotentialMaster
makeQFH(double) - Method in class etomica.potential.P2HePCKLJS
makeQFH(double) - Method in class etomica.potential.P2HeSimplified
makeQFH(double) - Method in class etomica.potential.P2NitrogenHellmann
makeReciprocal() - Method in class etomica.lattice.crystal.Primitive: Method defining and constructing reciprocal primitive;
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveBcc
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveCubic
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveFcc
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveGeneral
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
makeReciprocal() - Method in class etomica.models.hexane.PrimitiveHexane
makeReeHoover(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations: Creates a set of Ree-Hoover clusters from the given cluster.
makeReeHoover(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
makeRhoCluster(MayerFunction, boolean) - Method in class etomica.virial.cluster.ExternalVirialDiagrams
makeRhoDiagrams() - Method in class etomica.virial.cluster.ExternalVirialDiagrams
makeRhoDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
makeRhoDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
makeRhoDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagrams
makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix
makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix2
makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsPT
makeRhoDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
makeRhoDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
makeRotationTensor() - Method in interface etomica.space.ISpace: Constructs and returns a new RotationTensor appropriate to the space.
makeRotationTensor() - Method in class etomica.space.Space
makeRotationTensor() - Method in class etomica.space1d.Space1D
makeRotationTensor() - Method in class etomica.space2d.Space2D
makeRotationTensor() - Method in class etomica.space3d.Space3D
makeScaledCoordinates(ISpace, Basis, int[]) - Static method in class etomica.normalmode.BasisBigCell
makeSemiclassical(double) - Method in class etomica.models.co2.P2CO2H2OWheatley
makeSemiclassical(double) - Method in class etomica.models.co2.P2CO2Hellmann
makeSemiclassical(double) - Method in class etomica.models.water.P2WaterSzalewicz
makeSemiclassicalTI(double) - Method in class etomica.models.co2.P2CO2H2OWheatley
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
makeSingleVirialClusters(ClusterSum, MayerFunction[][], int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction[], int) - Method in class etomica.virial.cluster.VirialDiagramsPT
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
makeSingleVirialClustersMulti(ClusterSumMultibody, MayerFunction, MayerFunctionNonAdditive) - Method in class etomica.virial.cluster.VirialDiagrams
makeSingleWater() - Static method in class etomica.rotation.SingleDumbellRattle
makeSingleWater() - Static method in class etomica.rotation.SingleDumbellShake
makeSingleWater() - Static method in class etomica.rotation.SingleWater
makeSingleWater() - Static method in class etomica.rotation.SingleWaterMatrix
makeSingleWater() - Static method in class etomica.rotation.SingleWaterRattle
makeSingleWater() - Static method in class etomica.rotation.SingleWaterShake
makeSite(AbstractLattice, int[]) - Method in interface etomica.lattice.SiteFactory: Constructs a site for placement in a lattice.
makeSite(AbstractLattice, int[]) - Method in class etomica.nbr.cell.Cell.CellFactory
makeSite(AbstractLattice, int[]) - Method in class etomica.nbr.cell.molecule.CellMolecular.CellFactory
makeSpecies(ISimulation) - Method in class etomica.chem.models.Model: Creates a species in the given simulation and returns it.
makeSpecies(ISpace) - Method in class etomica.models.rowley.SpeciesFactoryEthanol
makeSpecies(ISpace) - Method in class etomica.models.rowley.SpeciesFactoryMethanol
makeSpecies(ISpace) - Method in class etomica.models.traPPE.SpeciesFactoryMethanol
makeSpecies(ISpace) - Method in interface etomica.virial.SpeciesFactory
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactoryOrientedSpheres
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactorySpheres
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactorySpheres2
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactoryTangentSpheres
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactoryWater3P
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactoryWater4P
makeSpecies(ISpace) - Method in class etomica.virial.SpeciesFactoryWaterGCPM
makeSpeciesInternal(ISimulation) - Method in class etomica.chem.models.Model: Internal method to be implemented by subclasses to create the actual Species object for the given Simulation.
makeSpeciesInternal(ISimulation) - Method in class etomica.chem.models.ModelChain
makeStuff(String, ParserLAMMPS.Options) - Static method in class etomica.parser.ParserLAMMPS
makeStuffFromLines(List<String>, ParserLAMMPS.Options) - Static method in class etomica.parser.ParserLAMMPS
makeTensor() - Method in interface etomica.space.ISpace: Constructs and returns a new Tensor appropriate to the space.
makeTensor() - Method in class etomica.space.Space
makeTensor() - Method in class etomica.space1d.Space1D
makeTensor() - Method in class etomica.space2d.Space2D
makeTensor() - Method in class etomica.space3d.Space3D
makeTI(double) - Method in class etomica.potential.P2HePCKLJS
makeTI(double) - Method in class etomica.potential.P2HeSimplified
makeTI(double) - Method in class etomica.potential.P2O2Bartolomei
makeUniqueElementSymbol(String) - Method in class etomica.simulation.Simulation: Returns an Element symbol starting with symbolBase that does not yet exist in the Simulation.
makeVector() - Method in interface etomica.space.ISpace: Constructs and returns a new Vector appropriate to the space.
makeVector(double[]) - Method in interface etomica.space.ISpace
makeVector(int[]) - Method in interface etomica.space.ISpace
makeVector() - Method in class etomica.space.Space
makeVector(int) - Static method in class etomica.space.Space: Returns a Vector from the space of the given dimension.
makeVector(double[]) - Method in class etomica.space.Space: Returns a Vector initialized to the given set of values in the array.
makeVector(int[]) - Method in class etomica.space.Space: Returns a Vector initialized to the given set of values in the array (cast to double).
makeVector() - Method in class etomica.space1d.Space1D
makeVector() - Method in class etomica.space2d.Space2D
makeVector() - Method in class etomica.space3d.Space3D
makeVectorArray(int) - Method in interface etomica.space.ISpace: Instance methods that makes and returns an array of vectors having the given number of elements.
makeVectorArray(int) - Method in class etomica.space.Space
makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
makeVirialCluster(MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialCluster(MayerFunction, MayerFunctionNonAdditive) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialCluster(MayerFunction, MayerFunctionNonAdditive, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialCluster(Set<Graph>, MayerFunction, MayerFunctionNonAdditive) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialCluster(MayerFunction[][], int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
makeVirialCluster(Set<Graph>, MayerFunction[][], int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
makeVirialCluster(MayerFunction, MayerFunction[]) - Method in class etomica.virial.cluster.VirialDiagramsPT
makeVirialCluster(Set<Graph>, MayerFunction, MayerFunction[]) - Method in class etomica.virial.cluster.VirialDiagramsPT
makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
makeVirialClusterHS(Set<Graph>, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialClusterSecondTemperatureDerivative(MayerFunction, MayerFunction, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialClusterTempDeriv(MayerFunction, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
makeVirialDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
makeVirialDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagrams
makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix
makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix2
makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsPT
makeVirialDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
makeWaterBox() - Static method in class etomica.rotation.WaterBox
makeWaterDroplet() - Static method in class etomica.rotation.WaterDroplet
makeWaterDroplet() - Static method in class etomica.rotation.WaterDropletMatrix
makeWaterDroplet() - Static method in class etomica.rotation.WaterDropletRattle
makeWaterDroplet() - Static method in class etomica.rotation.WaterDropletShake
makeWaterDroplet() - Static method in class etomica.rotation.WaterTrimer
makeWaterDroplet() - Static method in class etomica.rotation.WaterTrimerRattle
makeWaterDroplet() - Static method in class etomica.rotation.WaterTrimerShake
makeWaveVectors(IBox) - Method in interface etomica.normalmode.WaveVectorFactory: Tells the instance to make wave vectors appropriate for the given box.
makeWaveVectors(IBox) - Method in class etomica.normalmode.WaveVectorFactory1D
makeWaveVectors(IBox) - Method in class etomica.normalmode.WaveVectorFactory2D
makeWaveVectors(IBox) - Method in class etomica.normalmode.WaveVectorFactoryFcc
makeWaveVectors(IBox) - Method in class etomica.normalmode.WaveVectorFactoryFromFile
makeWaveVectors(IBox) - Method in class etomica.normalmode.WaveVectorFactorySimple
makeWaveVectors(IBox) - Method in class etomica.normalmode.WaveVectorFactorySuperBox
makeWeightCluster(ClusterAbstract[]) - Method in interface etomica.virial.ClusterWeight.Factory
makeWeightCluster(ClusterAbstract) - Static method in class etomica.virial.ClusterWeightAbs
makeWeightClusters(ClusterAbstract[]) - Static method in class etomica.virial.ClusterWeightAbs
makeWertheimCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
makeWertheimDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
makeWrapperObject(Class) - Method in class etomica.util.ReadParameters
manager - Variable in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
managerPanel - Variable in class etomica.modules.clustergenerator.MyApplet
map(IFunction) - Method in interface etomica.api.IVectorMutable: Applies the given function to each element of the vector.
map(IFunction) - Method in interface etomica.data.IData: Maps the function on all data values, replace each with the value given by the function applied to it.
map(IFunction) - Method in class etomica.data.types.DataDouble: Maps the function on this instance's value, replacing it with the value returned by the function.
map(IFunction) - Method in class etomica.data.types.DataDoubleArray: Replaces all values by the value of the function applied to each.
map(IFunction) - Method in class etomica.data.types.DataDoubleBDArray: Replaces all values by the value of the function applied to each.
map(IFunction) - Method in class etomica.data.types.DataGroup
map(IFunction) - Method in class etomica.data.types.DataTensor: Maps the function on all vector elements, replacing each with the value given by the function applied to it.
map(IFunction) - Method in class etomica.data.types.DataVector: Maps the function on all vector elements, replacing each with the value given by the function applied to it.
map(byte) - Method in class etomica.graph.operations.RelabelParameters
map(IFunction) - Method in interface etomica.space.Tensor
map(IFunction) - Method in class etomica.space1d.Tensor1D
map(IFunction) - Method in class etomica.space1d.Vector1D
map(IFunction) - Method in class etomica.space2d.Tensor2D
map(IFunction) - Method in class etomica.space2d.Vector2D
map(IFunction) - Method in class etomica.space3d.Tensor3D
map(IFunction) - Method in class etomica.space3d.Vector3D
map(IFunction) - Method in class etomica.spaceNd.TensorND
map(IFunction) - Method in class etomica.spaceNd.VectorND
MappedU - Class in etomica.mappedvirial
MappedU(ISpace, int, double, double, double) - Constructor for class etomica.mappedvirial.MappedU
MappedU.LJMDParams - Class in etomica.mappedvirial
MappedUpotential - Class in etomica.mappedvirial: PotentialCalculation that implements mapped-averaged virial (to get the pressure).
MappedUpotential(ISpace, IBox, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.MappedUpotential
MappedVirialLJ - Class in etomica.mappedvirial
MappedVirialLJ(ISpace, int, double, double, double) - Constructor for class etomica.mappedvirial.MappedVirialLJ
MappedVirialLJ.LJMDParams - Class in etomica.mappedvirial
MappedVirialLJVGr - Class in etomica.mappedvirial
MappedVirialLJVGr(ISpace, int, double, double, double) - Constructor for class etomica.mappedvirial.MappedVirialLJVGr
MappedVirialLJVGr.LJMDParams - Class in etomica.mappedvirial
mapValue(String) - Method in class org.jmol.script.ScriptVariable
markDirty() - Method in class etomica.util.numerical.AkimaSpline
markLines(String, char) - Static method in class org.jmol.util.Parser
MAROON - Static variable in class org.jmol.util.Colix
maskSingleBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong: Returns a long with a single bit set, corresponding to the bit offset of the given bit index.
maskSingleBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: Returns a long with a single bit set, corresponding to the bit offset of the given bit index.
maskSingleLong() - Method in class etomica.graph.model.impl.BitmapOfLong: Returns a bitmask corresponding to the valid bits of the long with the given index.
maskSingleLong(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: Returns a bitmask corresponding to the valid bits of the long with the given index.
mass - Variable in class etomica.chem.elements.ElementChemical
mass - Variable in class etomica.chem.elements.ElementSimple
mass - Static variable in class etomica.models.co2.P2CO2Hellmann
mass - Static variable in class etomica.models.water.P2WaterSzalewicz
mass - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
mass - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor
mass - Variable in class etomica.modules.swmd.SwmdGraphic
mass - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
mass - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
mass - Variable in class etomica.potential.P2HePCKLJS.P2HeQFH
mass - Variable in class etomica.potential.P2HePCKLJS.P2HeTI
mass - Variable in class etomica.potential.P2HeSimplified.P2HeQFH
mass - Variable in class etomica.potential.P2HeSimplified.P2HeTI
mass - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
mass - Variable in class etomica.species.SpeciesOriented
Mass - Class in etomica.units: Dimension for all units of mass.
mass() - Method in class etomica.units.systems.CGS
mass - Variable in class etomica.units.systems.LJ
mass() - Method in class etomica.units.systems.LJ
mass() - Method in class etomica.units.systems.MKS
mass() - Method in class etomica.units.systems.UnitSystem
mass() - Method in class etomica.units.systems.UnitSystem.Sim
mass - Static variable in class org.jmol.script.Token
mass0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
mass0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
mass1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
massBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
massBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
massBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
massBox - Variable in class etomica.modules.swmd.SwmdGraphic
MassEditor(SpeciesSpheresMono, String) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor
massH - Variable in class etomica.models.water.PNWaterGCPM
massH - Static variable in class etomica.virial.simulations.VirialH2PISimple
massMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
massN - Static variable in class etomica.virial.simulations.VirialN2
massN - Static variable in class etomica.virial.simulations.VirialN2PI
massN2 - Static variable in class etomica.potential.P2NitrogenHellmann
massO - Variable in class etomica.models.water.PNWaterGCPM
massO - Static variable in class etomica.virial.simulations.VirialO2PI
MassProductionVirialRowleyAlcohol - Class in etomica.models.rowley
MassProductionVirialRowleyAlcohol() - Constructor for class etomica.models.rowley.MassProductionVirialRowleyAlcohol
massSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
massSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
mat4 - Variable in class org.jmol.util.MeshSurface
Match - Class in etomica.graph.isomorphism
Match() - Constructor for class etomica.graph.isomorphism.Match
match(Graph, Graph, boolean) - Static method in class etomica.graph.isomorphism.Match: Execution of an isomorphism test with the default algorithm.
match(SearchState) - Static method in class etomica.graph.isomorphism.Match: Execution of an isomorphism test with a provided initial state.
MaterialFracture - Class in etomica.modules.materialfracture
MaterialFracture() - Constructor for class etomica.modules.materialfracture.MaterialFracture
MaterialFractureGraphic - Class in etomica.modules.materialfracture: Graphical components for Material Fracture module
MaterialFractureGraphic(MaterialFracture) - Constructor for class etomica.modules.materialfracture.MaterialFractureGraphic
MaterialFractureGraphic.Applet - Class in etomica.modules.materialfracture
Matrix - Class in etomica.math.linearalgebra: Compilation: javac Matrix.java Execution: java Matrix A bare-bones immutable data type for M-by-N matrices.
Matrix(int, int) - Constructor for class etomica.math.linearalgebra.Matrix
Matrix(double[][]) - Constructor for class etomica.math.linearalgebra.Matrix
matrix3f - Static variable in class org.jmol.script.Token
Matrix3f - Class in org.jmol.util: A single precision floating point 3 by 3 matrix.
Matrix3f() - Constructor for class org.jmol.util.Matrix3f: Constructs and initializes a Matrix3f to all zeros.
matrix4f - Static variable in class org.jmol.script.Token
Matrix4f - Class in org.jmol.util: A single precision floating point 4 by 4 matrix.
Matrix4f() - Constructor for class org.jmol.util.Matrix4f
MATRIX_A - Static variable in class etomica.util.RandomMersenneTwister
matrixPermutation(int[], int[][]) - Static method in class etomica.math.discrete.PermutationIterator: Returns a new matrix formed by permuting the rows and columns of the given matrix according to the permuation list p.
matrixToScript(Object) - Static method in class org.jmol.util.Escape
max - Variable in class etomica.lattice.IndexIteratorIncreasing
max(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Maximum of two values.
max(Vector<Ifactor>) - Static method in class etomica.veos.bigdecimal.Ifactor: Maximum of a list of values.
max(Rational) - Method in class etomica.veos.bigdecimal.Rational: Compares the value of this with another constant.
max - Static variable in class org.jmol.script.Token
MAX_INT - Static variable in class etomica.veos.bigdecimal.Rational: The maximum and minimum value of a standard Java integer, 2^31.
max_l - Variable in class etomica.potential.P2HydrogenPatkowski
max_l - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
MAX_X - Static variable in class etomica.graphics.DevicePlotPoints
MAX_Y - Static variable in class etomica.graphics.DevicePlotPoints
maxAngle - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
maxBias - Variable in class etomica.virial.MCMoveClusterAtomHSRing
maxBiasMinN - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
maxBiasR - Variable in class etomica.virial.MCMoveClusterAtomHSRing
maxBlocks - Variable in class etomica.data.AccumulatorAverageCollapsing
maxBlockSize - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
maxBlockSize - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
maxBlockSize - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
maxBonds - Variable in class etomica.association.AssociationHelperBranched
maxBonds - Variable in class etomica.association.AssociationHelperMolecule
maxcf - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
maxChainLength - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
maxChainLength - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
maxChainLength - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
maxCount - Variable in class etomica.graph.iterators.filters.FieldNodeCount
maxCount - Variable in class etomica.graph.property.FieldNodeCountMax
maxDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
maxDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
maxEta - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
maxExchangeNodes - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
maxFloat - Variable in class etomica.graphics.DisplayTable
maxHeight - Variable in class etomica.graph.view.rasterizer.SVGConverter: Maximum output image height.
maximum() - Method in class etomica.util.DoubleRange: The maximum defined by this range.
maximum() - Method in class etomica.util.IntegerRange: The maximum defined by this range.
MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JmolConstants
MAXIMUM_QUALITY - Static variable in class etomica.graph.view.rasterizer.SVGConverter: Maximum quality value
maxIndex - Variable in class etomica.box.Box
maxIndex() - Method in interface etomica.veos.BetaSource: Returns k such that beta[j] == 0 for all j > k.
maxIndex() - Method in class etomica.veos.HardRods
maxIndex() - Method in class etomica.veos.VanderWaals
maxIndex - Variable in class etomica.virial.cluster.PermutationIterator
maxInsertDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
maxInsertDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
MaxIsomorph - Class in etomica.graph.operations: Returns a set of graphs with each one corresponding to a graph in the original set.
MaxIsomorph() - Constructor for class etomica.graph.operations.MaxIsomorph
maxIsomorph - Variable in class etomica.graph.property.FFTDecomposition
maxIsomorph - Variable in class etomica.graph.property.IsFFT
MaxIsomorph.MaxIsomorphParameters - Class in etomica.graph.operations: Parameters class for MaxIsomorph which defines a graph operation and property to select for.
MaxIsomorphCriteriaMixture() - Constructor for class etomica.virial.cluster.VirialDiagramsMix2.MaxIsomorphCriteriaMixture
MaxIsomorphParameters(GraphOp, Property) - Constructor for class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
MaxIsomorphWertheim - Class in etomica.graph.operations: Returns a set of graphs with each one corresponding to a graph in the original set.
MaxIsomorphWertheim() - Constructor for class etomica.graph.operations.MaxIsomorphWertheim
MaxIsomorphWertheim.MaxIsomorphWertheimParameters - Class in etomica.graph.operations
MaxIsomorphWertheimParameters(CombineABSite.CombineABSiteParameters) - Constructor for class etomica.graph.operations.MaxIsomorphWertheim.MaxIsomorphWertheimParameters
MaxIsomorphWertheimParameters(Property, CombineABSite.CombineABSiteParameters) - Constructor for class etomica.graph.operations.MaxIsomorphWertheim.MaxIsomorphWertheimParameters
maxIterations - Variable in class etomica.integrator.IntegratorRigidIterative
maxIterations - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
maxIterations - Variable in class etomica.integrator.IntegratorVelocityVerletShake
maxIterations - Variable in class etomica.modules.interfacial.FitTanh
maxIterations - Variable in class etomica.surfacetension.FitTanh
maxLength - Variable in class etomica.association.MCMoveAtomMonomer
maxLength - Variable in class etomica.association.MCMoveAtomSmer
maxLength - Variable in class etomica.association.MCMoveMoleculeMonomer
maxLength - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
maxLength - Variable in class etomica.association.MCMoveMoleculeSmer
maxLength - Variable in class etomica.association.MCMoveRotateAssociated
maxLPN - Static variable in class etomica.math.SpecialFunctions
maxMolecule - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
maxN - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
maxNbrsVapor - Variable in class etomica.modules.droplet.AtomFilterLiquidAtomic
maxNumAtoms - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
maxNumAtoms - Variable in class etomica.virial.PotentialEmulCached
maxNumBeads - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
maxpar1 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
maxpar2 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
maxPhi - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
maxRatio - Variable in class etomica.data.DataPumpListenerPow
maxRunNumber - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
maxRunNumber - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
maxSample - Variable in class etomica.data.AccumulatorAverageCollapsingLogAB
maxSampleValue - Variable in class etomica.virial.MeterVirialBDBin
maxSleep - Variable in class etomica.graphics.DeviceDelaySlider
maxSphereCache - Static variable in class org.jmol.util.Shader
maxSteps - Variable in class etomica.action.ActionIntegrate
maxSteps - Variable in class etomica.action.activity.ActivityIntegrate
maxVacancy - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
MaxwellBoltzmann - Class in etomica.statmech: Non-instantiable class with static methods for implementing features of the Maxwell-Boltzmann velocity distribution.
MaxwellBoltzmann.Distribution - Class in etomica.statmech: Function giving the Maxwell-Boltzmann distribution of speeds.
maxWidth - Variable in class etomica.graph.view.rasterizer.SVGConverter: Maximum output image width.
maxwidth - Variable in class etomica.util.ScientificFormat
maybeTrimToSize() - Method in class etomica.atom.AtomArrayList
maybeTrimToSize() - Method in class etomica.atom.MoleculeArrayList
MayerD2FDT2Spherical - Class in etomica.virial: Required for computing second derivatives of virial coefficients w/r to temperature
MayerD2FDT2Spherical(Potential2Spherical) - Constructor for class etomica.virial.MayerD2FDT2Spherical: Constructor for MayerESpherical.
MayerDFDTSpherical - Class in etomica.virial: Required for computing temperature derivatives of virial coefficients
MayerDFDTSpherical(Potential2Spherical) - Constructor for class etomica.virial.MayerDFDTSpherical: Constructor for MayerESpherical.
MayerDFQFHDTSpherical - Class in etomica.virial: Required for computing temperature derivatives of virial coefficients computed with quadratic Feynmann-Hibbs modification to the potential.
MayerDFQFHDTSpherical(P2EffectiveFeynmanHibbs) - Constructor for class etomica.virial.MayerDFQFHDTSpherical: Constructor for MayerESpherical.
MayerEGeneral - Class in etomica.virial
MayerEGeneral(IPotentialMolecular) - Constructor for class etomica.virial.MayerEGeneral: Constructor Mayer function using given potential.
MayerEHardSphere - Class in etomica.virial
MayerEHardSphere() - Constructor for class etomica.virial.MayerEHardSphere: Constructor for MayerEHardSphere.
MayerEHardSphere(double) - Constructor for class etomica.virial.MayerEHardSphere
MayerENonGeneral - Class in etomica.virial
MayerENonGeneral(IPotentialMolecular, double) - Constructor for class etomica.virial.MayerENonGeneral: Constructor Mayer function using given potential.
MayerESpherical - Class in etomica.virial
MayerESpherical(Potential2Spherical) - Constructor for class etomica.virial.MayerESpherical: Constructor for MayerESpherical.
MayerFunction - Interface in etomica.virial
MayerFunctionMolecularThreeBody - Class in etomica.virial
MayerFunctionMolecularThreeBody(IPotentialMolecular) - Constructor for class etomica.virial.MayerFunctionMolecularThreeBody
MayerFunctionNonAdditive - Interface in etomica.virial: Interface for a Mayer f-function, which takes 3+ atoms and returns exp(-(u(atoms)-u(pairs))/kT) - 1
MayerFunctionNonAdditiveFull - Class in etomica.virial
MayerFunctionNonAdditiveFull(IPotentialMolecular) - Constructor for class etomica.virial.MayerFunctionNonAdditiveFull
MayerFunctionProductGeneral - Class in etomica.virial
MayerFunctionProductGeneral(ISpace, MayerFunction[], double[]) - Constructor for class etomica.virial.MayerFunctionProductGeneral
MayerFunctionSphericalThreeBody - Class in etomica.virial: Non-additive Mayer function class for "spherical" potentials
MayerFunctionSphericalThreeBody(IPotentialAtomicMultibody) - Constructor for class etomica.virial.MayerFunctionSphericalThreeBody
MayerFunctionSum - Class in etomica.virial
MayerFunctionSum(MayerFunction[], double[]) - Constructor for class etomica.virial.MayerFunctionSum
MayerFunctionSumGeneral - Class in etomica.virial
MayerFunctionSumGeneral(ISpace, MayerFunction[], double[]) - Constructor for class etomica.virial.MayerFunctionSumGeneral
MayerFunctionTemperature - Class in etomica.virial: Mayer function that wraps another MayerFunction and ignores the temperature passed to f(), asking the wrapped MayerFunction for its value at the MayerFunction Temperature's temperature.
MayerFunctionTemperature(MayerFunction, double) - Constructor for class etomica.virial.MayerFunctionTemperature
MayerFunctionThreeBody - Class in etomica.virial: This class acts as a non-additive Mayer function for molecules that interact with only a 3-body potential.
MayerFunctionThreeBody() - Constructor for class etomica.virial.MayerFunctionThreeBody
MayerGeneral - Class in etomica.virial
MayerGeneral(IPotentialMolecular) - Constructor for class etomica.virial.MayerGeneral: Constructor Mayer function using given potential.
MayerGeneralAtomic - Class in etomica.virial
MayerGeneralAtomic(IPotentialAtomic) - Constructor for class etomica.virial.MayerGeneralAtomic: Constructor Mayer function using given potential.
MayerGeneralSpherical - Class in etomica.virial
MayerGeneralSpherical(Potential2Spherical) - Constructor for class etomica.virial.MayerGeneralSpherical: Constructor Mayer function using given potential.
MayerHardSphere - Class in etomica.virial
MayerHardSphere() - Constructor for class etomica.virial.MayerHardSphere: Constructor for MayerHardSphere.
MayerHardSphere(double) - Constructor for class etomica.virial.MayerHardSphere
MayerIonicDiagram1qbond - Class in etomica.virial.cluster: modified from WertheimNaphthalene class cluster diagrams generator for ionic solutions, based on Mayer's theory f-bond is splitted to k-bond, (kg1+g1) diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded) g1/kg1 is magically changed to represent q1-bond [exp(-kappa * r / (4*pi*r)] with different domain, but g1 is still in use kg1 represents [exp(-kappa * r / (4*pi*r)] instead of [exp(-alpha * r / (4*pi*r)] (kq1 essentially) ===> then q1 is substituted by (xq1-kg1), where xq1 has domain:[sigmaHS, infinity] qi represent xqi bonds, gi represent REAL q bonds the final result contains q1(represent xq1) and kg1(represent q1) can handle 4pt just xq1 & kq1 & k in the final set of S
MayerIonicDiagram1qbond(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram1qbond
MayerIonicDiagram1qbond(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram1qbond
MayerIonicDiagram2qbonds - Class in etomica.virial.cluster: Mayer's theory on ionic solution f-bond is splitted to k-bond, (kg+g),(kg2+g2) diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded) gi is substituted by (qi - kgi) qi represent modified q bonds, gi represent REAL q bonds even number of q bonds , the final result contains q1,q2,kg1,kg2bonds
MayerIonicDiagram2qbonds(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram2qbonds
MayerIonicDiagram2qbonds(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram2qbonds
MayerIonicDiagram4qbonds - Class in etomica.virial.cluster: cluster diagrams generator for ionic solutions, based on Mayer's theory f-bond is split into k-bond(HS f-hond), (kg+g),(kg2+g2),(kg3+g3),(kg4+g4)truncation diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded) gi is substituted by (qi - kgi), where qi represents modified q bonds( domain [sigmaHS,infinity), gi represent REAL q bonds, i represents q bonds power the final sets of diagrams contains q1,q2,q3,q4;kg1,kg2,kg3,kg4 bonds 2 pt diagrams with q2 bond is discarded ( cycle diagram) cannot handle 4 points due to the insufficiency of calculations
MayerIonicDiagram4qbonds(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram4qbonds
MayerIonicDiagram4qbonds(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram4qbonds
MayerPTAtt - Class in etomica.virial: Mayer function class that returns temperature expansion bond of the desired order using molecular potentials.
MayerPTAtt(IPotentialMolecular, IPotentialMolecular, int) - Constructor for class etomica.virial.MayerPTAtt: Constructor takes reference potential, attractive component and order in temperature.
MayerPUGeneral - Class in etomica.virial: f + u f: exp(-beta U) u: 0 for r < sigmaHS, dipole energy otherwise a Potential2 object.
MayerPUGeneral(ISpace, double, double, IPotentialMolecular) - Constructor for class etomica.virial.MayerPUGeneral
MayerSphericalPlus - Class in etomica.virial
MayerSphericalPlus(Potential2Spherical, Potential2Spherical) - Constructor for class etomica.virial.MayerSphericalPlus: Constructor Mayer function using given potential.
MayerSphericalPTAtt - Class in etomica.virial: Mayer function class that returns temperature expansion bond of the desired order.
MayerSphericalPTAtt(Potential2Spherical, Potential2Spherical, int) - Constructor for class etomica.virial.MayerSphericalPTAtt: Constructor takes reference potential, attractive component and order in temperature.
MayerSSSeries - Class in etomica.virial
MayerSSSeries(int) - Constructor for class etomica.virial.MayerSSSeries: Constructor for MayerHardSphere.
MayerWell - Class in etomica.virial
MayerWell(double, double) - Constructor for class etomica.virial.MayerWell
MayerXSpherical - Class in etomica.virial
MayerXSpherical(Potential2SoftSpherical) - Constructor for class etomica.virial.MayerXSpherical: Constructor for MayerESpherical.
mBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
mBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
mBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
mBond - Variable in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
mBond - Variable in class etomica.virial.cluster.VirialDiagrams
mBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
MBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
mBond - Variable in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
mBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
mBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
mBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mc - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
mc - Variable in class etomica.virial.ClusterWheatleySoftBD
mc - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
mc - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
mCapF1Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCapF2Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCapFACBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFACBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCapFBCBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFBCBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCapFBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCapFCABond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFCABond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCapFCBBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mCapFCBBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mCluster - Variable in class etomica.virial.cluster.ClusterGenerator
MCMove - Class in etomica.integrator.mcmove: Parent class for all elementary Monte Carlo move classes, as used by IntegratorMC class.
MCMove(IPotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMove
MCMove(IPotentialMaster, MCMoveTracker) - Constructor for class etomica.integrator.mcmove.MCMove
mcMove - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
mcMove - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
mcMove - Variable in class etomica.interfacial.LJMD
mcMove - Variable in class etomica.normalmode.MeterSamplingHarmonic
mcMove - Variable in class etomica.normalmode.MeterSamplingTarget
mcMove - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
mcMove - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
mcmove - Variable in class etomica.spin.Heisenberg
mcMove - Variable in class etomica.virial.MCMoveClusterAtomQ
mcMoveAtom - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
mcMoveAtom - Variable in class etomica.densityofstate.DensityOfState
mcMoveAtom - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
mcMoveAtom - Variable in class etomica.freeenergy.npath.SimIdealGas
mcMoveAtom - Variable in class etomica.freeenergy.npath.SimLJ
MCMoveAtom - Class in etomica.integrator.mcmove: Standard Monte Carlo atom-displacement trial move.
MCMoveAtom(IRandom, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveAtom
MCMoveAtom(IPotentialMaster, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.integrator.mcmove.MCMoveAtom
MCMoveAtom(IPotentialMaster, MeterPotentialEnergy, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.integrator.mcmove.MCMoveAtom
mcMoveAtom - Variable in class etomica.liquidLJ.LjMC3D
mcMoveAtom - Variable in class etomica.metastable.LJNPT
mcMoveAtom - Variable in class etomica.metastable.LJNVT
mcMoveAtom - Variable in class etomica.modules.ensembles.LJMC
mcMoveAtom - Variable in class etomica.simulation.prototypes.HsMc2d
mcMoveAtom - Variable in class etomica.simulation.prototypes.SoftSphere3d
mcMoveAtom - Variable in class etomica.surfacetension.LJMC
mcMoveAtom - Variable in class etomica.tests.TestLJMC3D
mcMoveAtom - Variable in class etomica.threaded.atom.LJMD3DThreaded
mcMoveAtom - Variable in class etomica.threaded.domain.LJMD3DThreaded
mcMoveAtom - Variable in class etomica.yukawa.TestHC2YukawaMC3D
mcMoveAtom - Variable in class etomica.yukawa.TestYukawaMC3D
MCMoveAtomAdjacent - Class in etomica.modules.entropylottery: Monte Carlo move that moves an atom by +/- 1 unit in a random dimension.
MCMoveAtomAdjacent(IRandom, ISpace) - Constructor for class etomica.modules.entropylottery.MCMoveAtomAdjacent
mcMoveAtomBigStep - Variable in class etomica.surfacetension.LJMC
MCMoveAtomCoupled - Class in etomica.freeenergy.npath: Created by andrew on 4/11/17.
MCMoveAtomCoupled(IRandom, IPotentialMaster, ISpace) - Constructor for class etomica.freeenergy.npath.MCMoveAtomCoupled
MCMoveAtomCoupled(IPotentialMaster, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.freeenergy.npath.MCMoveAtomCoupled
MCMoveAtomCoupled(IPotentialMaster, MeterPotentialEnergy, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.freeenergy.npath.MCMoveAtomCoupled
mcMoveAtomCoupled - Variable in class etomica.freeenergy.npath.SimIdealGas
mcMoveAtomCoupled - Variable in class etomica.freeenergy.npath.SimLJ
MCMoveAtomCoupled - Class in etomica.normalmode: Standard Monte Carlo atom-displacement trial move.
MCMoveAtomCoupled(IPotentialMaster, MeterPotentialEnergy, IRandom, ISpace) - Constructor for class etomica.normalmode.MCMoveAtomCoupled
MCMoveAtomCoupledBennet - Class in etomica.normalmode: Standard Monte Carlo atom-displacement trial move.
MCMoveAtomCoupledBennet(IPotentialMaster, IRandom, CoordinateDefinition, NormalModes, double, ISpace) - Constructor for class etomica.normalmode.MCMoveAtomCoupledBennet
MCMoveAtomCoupledUmbrella - Class in etomica.normalmode: Standard Monte Carlo atom-displacement trial move.
MCMoveAtomCoupledUmbrella(IPotentialMaster, IRandom, CoordinateDefinition, NormalModes, double, ISpace) - Constructor for class etomica.normalmode.MCMoveAtomCoupledUmbrella
MCMoveAtomDimer - Class in etomica.association
MCMoveAtomDimer(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveAtomDimer
MCMoveAtomDimer(IPotentialMaster, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.association.MCMoveAtomDimer
mcMoveAtomDimer - Variable in class etomica.association.TestLJAssociationMC3D_NPT
mcMoveAtomDimer - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveAtomInRegion - Class in etomica.integrator.mcmove: MC move that operates only on atoms within a given region of x values.
MCMoveAtomInRegion(IRandom, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveAtomInRegion
MCMoveAtomMonomer - Class in etomica.association
MCMoveAtomMonomer(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveAtomMonomer
MCMoveAtomMonomer(IPotentialMaster, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.association.MCMoveAtomMonomer
mcMoveAtomMonomer - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveAtomMonomer - Variable in class etomica.association.TestLJAssociationMC3D_NPT
mcMoveAtomMonomer - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
mcMoveAtomMonomer - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveAtomNbr - Class in etomica.interfacial
MCMoveAtomNbr(IRandom, IPotentialMaster, ISpace) - Constructor for class etomica.interfacial.MCMoveAtomNbr
MCMoveAtomNoSmer - Class in etomica.association
MCMoveAtomNoSmer(IRandom, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveAtomNoSmer
MCMoveAtomNPath - Class in etomica.freeenergy.npath: Created by andrew on 4/11/17.
MCMoveAtomNPath(IRandom, PotentialMaster, ISpace, P1ImageHarmonic) - Constructor for class etomica.freeenergy.npath.MCMoveAtomNPath
MCMoveAtomSmer - Class in etomica.association
MCMoveAtomSmer(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveAtomSmer
MCMoveAtomSmer(IPotentialMaster, IRandom, ISpace, double, double, boolean) - Constructor for class etomica.association.MCMoveAtomSmer
mcMoveAtomSmer - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveAtomSmer - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
MCMoveAtomSuperBox - Class in etomica.normalmode: Standard Monte Carlo atom-displacement trial move.
MCMoveAtomSuperBox(IPotentialMaster, IRandom, ISpace, CoordinateDefinitionLeafSuperBox) - Constructor for class etomica.normalmode.MCMoveAtomSuperBox
MCMoveAtomSwap - Class in etomica.freeenergy.npath: Created by andrew on 4/11/17.
MCMoveAtomSwap(IRandom, IPotentialMaster, ISpace, P1ImageHarmonic) - Constructor for class etomica.freeenergy.npath.MCMoveAtomSwap
mcMoveBiasUB - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
MCMoveBiasUB - Class in etomica.association
MCMoveBiasUB(PotentialMasterCell, BiasVolume, IRandom, ISpace) - Constructor for class etomica.association.MCMoveBiasUB
mcMoveBiasUB - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveBiasUB - Variable in class etomica.association.TestLJAssociationMC3D_NPT
mcMoveBiasUB - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
mcMoveBiasUB - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveBiasUBMolecule - Class in etomica.association
MCMoveBiasUBMolecule(PotentialMaster, BiasVolumeMolecule, IRandom, ISpace) - Constructor for class etomica.association.MCMoveBiasUBMolecule
MCMoveBox - Class in etomica.integrator.mcmove: MCMove parent class for moves that operate on a single Box.
MCMoveBox(IPotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMoveBox
MCMoveBox(IPotentialMaster, MCMoveTracker) - Constructor for class etomica.integrator.mcmove.MCMoveBox
MCMoveBoxSize - Class in etomica.integrator.mcmove: Monte Carlo move for changing the box dimensions at constant volume.
MCMoveBoxSize(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveBoxSize
MCMoveBoxSize(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveBoxSize
MCMoveBoxStep - Class in etomica.integrator.mcmove: MCMove parent class for moves that have a step size and operate on a single Box.
MCMoveBoxStep(IPotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMoveBoxStep
MCMoveBoxStep(IPotentialMaster, MCMoveStepTracker) - Constructor for class etomica.integrator.mcmove.MCMoveBoxStep
MCMoveCBMC - Class in etomica.models.hexane
MCMoveCBMC(IPotentialMaster, IRandom, ISpace, IntegratorMC, IBox, int, int) - Constructor for class etomica.models.hexane.MCMoveCBMC
MCMoveChangeBondLength - Class in etomica.virial
MCMoveChangeBondLength(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveChangeBondLength
MCMoveChangeMultipleModes - Class in etomica.models.oneDHardRods: A Monte Carlo move which selects a wave vector and mode(s), and changes the normal mode associated with that wave vector and mode(s).
MCMoveChangeMultipleModes(IPotentialMaster, IRandom) - Constructor for class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
MCMoveChangeMultipleWV - Class in etomica.models.oneDHardRods: A Monte Carlo move which selects a wave vector, and changes the normal modes associated with that wave vector.
MCMoveChangeMultipleWV(IPotentialMaster, IRandom) - Constructor for class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
MCMoveClusterAngleBend - Class in etomica.virial: An MC Move for cluster simulations that bends the bond angle for 3-atom molecule.
MCMoveClusterAngleBend(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.virial.MCMoveClusterAngleBend
MCMoveClusterAngleBend(IPotentialMaster, IRandom, double, ISpace) - Constructor for class etomica.virial.MCMoveClusterAngleBend
MCMoveClusterAngleBendAceticAcid - Class in etomica.virial: An MC Move for cluster simulations that bends the bond angle for 3-atom molecule.
MCMoveClusterAngleBendAceticAcid(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.virial.MCMoveClusterAngleBendAceticAcid
MCMoveClusterAngleBendAceticAcid(IPotentialMaster, IRandom, double, ISpace) - Constructor for class etomica.virial.MCMoveClusterAngleBendAceticAcid
MCMoveClusterAtom - Class in etomica.virial: Overrides MCMoveAtom to prevent index-0 molecule from being displaced
MCMoveClusterAtom(IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterAtom
MCMoveClusterAtomChainHSTail - Class in etomica.virial: Grows configurations of chains with the pair probability distribution that is flat for some distance and then has a power-law decay tail.
MCMoveClusterAtomChainHSTail(IRandom, ISpace, double, double) - Constructor for class etomica.virial.MCMoveClusterAtomChainHSTail
MCMoveClusterAtomDiscrete - Class in etomica.virial: Extension of MCMoveClusterAtom that moves only the second atom and only along the x axis.
MCMoveClusterAtomDiscrete(IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveClusterAtomDiscrete
MCMoveClusterAtomHSChain - Class in etomica.virial
MCMoveClusterAtomHSChain(IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveClusterAtomHSChain
MCMoveClusterAtomHSRing - Class in etomica.virial
MCMoveClusterAtomHSRing(IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveClusterAtomHSRing
MCMoveClusterAtomHSTree - Class in etomica.virial
MCMoveClusterAtomHSTree(IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveClusterAtomHSTree
MCMoveClusterAtomMulti - Class in etomica.virial
MCMoveClusterAtomMulti(IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterAtomMulti
MCMoveClusterAtomQ - Class in etomica.virial
MCMoveClusterAtomQ(IRandom, ISpace, MCMoveAtom) - Constructor for class etomica.virial.MCMoveClusterAtomQ
MCMoveClusterAtomRotateMulti - Class in etomica.virial: Extension of MCMoveAtom that does trial in which several atom orientations are perturbed.
MCMoveClusterAtomRotateMulti(IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterAtomRotateMulti
MCMoveClusterDiagram - Class in etomica.virial: Move that attempts to perform changes in the cluster diagram.
MCMoveClusterDiagram(IPotentialMaster) - Constructor for class etomica.virial.MCMoveClusterDiagram
MCMoveClusterMolecule - Class in etomica.virial: Standard Monte Carlo molecule-displacement trial move for cluster integrals.
MCMoveClusterMolecule(ISimulation, ISpace) - Constructor for class etomica.virial.MCMoveClusterMolecule
MCMoveClusterMolecule(IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveClusterMolecule
MCMoveClusterMoleculeLayerMove - Class in etomica.virial: Monte Carlo molecule-displacement from 1 layer to the other layer trial move for cluster integrals.
MCMoveClusterMoleculeLayerMove(ISimulation, ISpace) - Constructor for class etomica.virial.MCMoveClusterMoleculeLayerMove
MCMoveClusterMoleculeMulti - Class in etomica.virial
MCMoveClusterMoleculeMulti(ISimulation, ISpace) - Constructor for class etomica.virial.MCMoveClusterMoleculeMulti
MCMoveClusterMoleculeMulti(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.virial.MCMoveClusterMoleculeMulti: Constructor for MCMoveAtomMulti.
MCMoveClusterPolyhedraChain - Class in etomica.virial
MCMoveClusterPolyhedraChain(IRandom, ISpace, double, IPotentialAtomic, double[][]) - Constructor for class etomica.virial.MCMoveClusterPolyhedraChain
MCMoveClusterPolyhedraTree - Class in etomica.virial
MCMoveClusterPolyhedraTree(IRandom, ISpace, double, IPotentialAtomic, double[][]) - Constructor for class etomica.virial.MCMoveClusterPolyhedraTree
MCMoveClusterReptateMulti - Class in etomica.virial: An MC move for cluster simulations which performs reptation moves on molecules.
MCMoveClusterReptateMulti(ISimulation, IPotentialMaster, int) - Constructor for class etomica.virial.MCMoveClusterReptateMulti
MCMoveClusterReptateMulti(IPotentialMaster, IRandom, int) - Constructor for class etomica.virial.MCMoveClusterReptateMulti: Constructor for MCMoveAtomMulti.
MCMoveClusterRingPartialRegrow - Class in etomica.virial: MCMove that partially regrows the beads of a ring polymer, accepting or rejecting the move based on the sampling weight.
MCMoveClusterRingPartialRegrow(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterRingPartialRegrow
MCMoveClusterRingPartialRegrow(IPotentialMaster, IRandom, ISpace, int[][]) - Constructor for class etomica.virial.MCMoveClusterRingPartialRegrow
MCMoveClusterRingRegrow - Class in etomica.virial: MCMove that fully regrows the beads of a ring polymer, accepting or rejecting the move based on the sampling weight.
MCMoveClusterRingRegrow(IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterRingRegrow
MCMoveClusterRingRegrow(IRandom, ISpace, int[][]) - Constructor for class etomica.virial.MCMoveClusterRingRegrow
MCMoveClusterRingRegrowExchange - Class in etomica.virial: MCMove that fully regrows the beads of a ring polymer, accepting or rejecting the move based on the sampling weight.
MCMoveClusterRingRegrowExchange(IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterRingRegrowExchange
MCMoveClusterRingRegrowOrientation - Class in etomica.virial: MCMove that fully regrows the beads of a ring polymer by rotating the images, accepting or rejecting the move based on the sampling weight.
MCMoveClusterRingRegrowOrientation(IRandom, ISpace, int) - Constructor for class etomica.virial.MCMoveClusterRingRegrowOrientation
MCMoveClusterRingScale - Class in etomica.virial: MCMove that scales the atoms of a molecule in or out.
MCMoveClusterRingScale(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterRingScale
MCMoveClusterRingScale(IPotentialMaster, IRandom, ISpace, int[][]) - Constructor for class etomica.virial.MCMoveClusterRingScale
MCMoveClusterRotateCH3 - Class in etomica.virial: Monte Carlo CH3 rotation for cluster integrals(Alkane TraPPE-EH).
MCMoveClusterRotateCH3(ISimulation, IPotentialMaster, int, ISpace) - Constructor for class etomica.virial.MCMoveClusterRotateCH3
MCMoveClusterRotateCH3(IPotentialMaster, IRandom, double, int, ISpace) - Constructor for class etomica.virial.MCMoveClusterRotateCH3
MCMoveClusterRotateMolecule3D - Class in etomica.virial: MC move for Mayer Sampling that rotates a single molecule
MCMoveClusterRotateMolecule3D(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterRotateMolecule3D
MCMoveClusterRotateMoleculeMulti - Class in etomica.virial: MCMove for use in a Mayer sampling simulation that rotates all molecules in a Box except the first molecule, which is never moved.
MCMoveClusterRotateMoleculeMulti(IRandom, ISpace) - Constructor for class etomica.virial.MCMoveClusterRotateMoleculeMulti
MCMoveClusterTorsionAceticAcid - Class in etomica.virial: An MC Move for cluster simulations that performs torsion moves on acetic acid.
MCMoveClusterTorsionAceticAcid(IPotentialMaster, ISpace, IRandom) - Constructor for class etomica.virial.MCMoveClusterTorsionAceticAcid: Constructor for MCMoveAtomMulti.
MCMoveClusterTorsionAlkaneEH - Class in etomica.virial: MC move for alkane-TraPPE-EH torsion pick up carbons in the box only, but move update all the atoms(carbons and hydrogens)
MCMoveClusterTorsionAlkaneEH(ISimulation, IPotentialMaster, ISpace, P4BondTorsion) - Constructor for class etomica.virial.MCMoveClusterTorsionAlkaneEH
MCMoveClusterTorsionAlkaneEH(IPotentialMaster, ISpace, IRandom, double, P4BondTorsion, int) - Constructor for class etomica.virial.MCMoveClusterTorsionAlkaneEH: Constructor for MCMoveAtomMulti.
MCMoveClusterTorsionMulti - Class in etomica.virial: An MC Move for cluster simulations that performs torsion moves on a chain molecule (of length N>=4).
MCMoveClusterTorsionMulti(ISimulation, IPotentialMaster, ISpace, P4BondTorsion) - Constructor for class etomica.virial.MCMoveClusterTorsionMulti
MCMoveClusterTorsionMulti(IPotentialMaster, ISpace, IRandom, double, P4BondTorsion, int) - Constructor for class etomica.virial.MCMoveClusterTorsionMulti: Constructor for MCMoveAtomMulti.
MCMoveClusterWiggleAceticAcid - Class in etomica.virial: An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveClusterWiggleAceticAcid(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.virial.MCMoveClusterWiggleAceticAcid
MCMoveClusterWiggleAceticAcid(IPotentialMaster, IRandom, double, ISpace) - Constructor for class etomica.virial.MCMoveClusterWiggleAceticAcid: Constructor for MCMoveAtomMulti.
MCMoveClusterWiggleAlkaneEH - Class in etomica.virial: Wiggle move for alkane, TraPPE-EH hydrogens attached to the 3 carbons are updated, keeping bond lengths and angles fixed *********** outline ************ // update j if j == 0 or j == n-1 // update 3 H on j // if j==0, update 2H on (j+1) // if j==n-1, update 2H on (j-1) && 0
MCMoveClusterWiggleAlkaneEH(ISimulation, IPotentialMaster, int, ISpace) - Constructor for class etomica.virial.MCMoveClusterWiggleAlkaneEH
MCMoveClusterWiggleAlkaneEH(IPotentialMaster, IRandom, double, int, ISpace) - Constructor for class etomica.virial.MCMoveClusterWiggleAlkaneEH: Constructor for MCMoveAtomMulti.
MCMoveClusterWiggleMulti - Class in etomica.virial: An MC Move for cluster simulations that "wiggles" a chain molecule.
MCMoveClusterWiggleMulti(ISimulation, IPotentialMaster, int, ISpace) - Constructor for class etomica.virial.MCMoveClusterWiggleMulti
MCMoveClusterWiggleMulti(IPotentialMaster, IRandom, double, int, ISpace) - Constructor for class etomica.virial.MCMoveClusterWiggleMulti: Constructor for MCMoveAtomMulti.
MCMoveCombinedCbmcTranslation - Class in etomica.models.hexane: MC move which performs a configuration bias monte carlo moved, then moves that atom to a new position so that its center of mass does not change.
MCMoveCombinedCbmcTranslation(IPotentialMaster, MCMoveCBMC, IRandom, ISpace) - Constructor for class etomica.models.hexane.MCMoveCombinedCbmcTranslation
MCMoveCombinedCbmcTranslation(IPotentialMaster, MCMoveCBMC, IRandom, IBox, ISpace) - Constructor for class etomica.models.hexane.MCMoveCombinedCbmcTranslation
MCMoveCompareMultipleWV - Class in etomica.models.oneDHardRods: A Monte Carlo move which compares several normal modes to harmonic normal modes and then explores the phase space defined by the remaining normal modes.
MCMoveCompareMultipleWV(IPotentialMaster, IRandom) - Constructor for class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
mcMoveDiagram - Variable in class etomica.virial.simulations.SimulationVirialDiagram
MCMoveDimer - Class in etomica.association: Standard Monte Carlo atom-displacement trial move of dimer
MCMoveDimer(ISimulation, PotentialMasterCell, ISpace, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimer
MCMoveDimer(PotentialMasterCell, IRandom, ISpace, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimer
mcMoveDimer - Variable in class etomica.association.TestLJAssociationMC3D_NPT
mcMoveDimer - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
MCMoveDimer - Class in etomica.integrator.mcmove: Standard Monte Carlo atom-displacement trial move.
MCMoveDimer(ISimulation, PotentialMasterCell, ISpace, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimer
MCMoveDimer(PotentialMasterCell, IRandom, ISpace, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimer
mcMoveDimer - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveDimerRotate - Class in etomica.association: Standard Monte Carlo atom-displacement trial move.
MCMoveDimerRotate(ISimulation, PotentialMasterCell, ISpace, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimerRotate
MCMoveDimerRotate(PotentialMasterCell, IRandom, ISpace, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimerRotate
mcMoveDimerRotate - Variable in class etomica.association.TestLJAssociationMC3D_NPT
mcMoveDimerRotate - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
MCMoveDimerRotate - Class in etomica.integrator.mcmove: Standard Monte Carlo atom-displacement trial move.
MCMoveDimerRotate(ISimulation, PotentialMasterCell, ISpace, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimerRotate
MCMoveDimerRotate(PotentialMasterCell, IRandom, ISpace, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimerRotate
mcMoveDimerRotate - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveEinsteinCrystal - Class in etomica.normalmode: MC move whose purpose in life is to sample an Einstein crystal.
MCMoveEinsteinCrystal(ISpace, IRandom) - Constructor for class etomica.normalmode.MCMoveEinsteinCrystal
MCMoveEvent - Class in etomica.integrator.mcmove
MCMoveEvent() - Constructor for class etomica.integrator.mcmove.MCMoveEvent
MCMoveEventManager - Class in etomica.integrator.mcmove
MCMoveEventManager() - Constructor for class etomica.integrator.mcmove.MCMoveEventManager
MCMoveHarmonic - Class in etomica.normalmode
MCMoveHarmonic(IRandom) - Constructor for class etomica.normalmode.MCMoveHarmonic
mcMoveHarmonic - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
mcMoveHarmonic - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
mcMoveHarmonic - Variable in class etomica.normalmode.MeterHarmonicEnergyFromMove
mcMoveHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
mcMoveHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
mcMoveHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
MCMoveHarmonicEin - Class in etomica.normalmode: MC move whose purpose in life is to sample a system whose energy is a combination of normal mode contributions and Einstein crystal contributions.
MCMoveHarmonicEin(IRandom) - Constructor for class etomica.normalmode.MCMoveHarmonicEin
MCMoveHarmonicStep - Class in etomica.normalmode: MCMove that performs random displacements in the harmonic coordinates for the k=0 wave vector.
MCMoveHarmonicStep(IPotentialMaster, IRandom) - Constructor for class etomica.normalmode.MCMoveHarmonicStep
mcMoveHarmonicStep - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
mcMoveHarmonicStep - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
mcMoveID - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
mcMoveID - Variable in class etomica.metastable.LJmuVT
mcMoveID - Variable in class etomica.modules.ensembles.LJMC
mcMoveID - Variable in class etomica.normalmode.DataSourceImposedFEFit
mcMoveID - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
mcMoveID - Variable in class etomica.normalmode.SimHSMDVacancy
mcMoveID - Variable in class etomica.normalmode.SimLJVacancy
mcMoveIDA - Variable in class etomica.modules.adsorption.Adsorption
mcMoveIDB - Variable in class etomica.modules.adsorption.Adsorption
MCMoveIDBiasAction - Class in etomica.integrator.mcmove: IAction which takes data from an MCMoveOverlapListener about acceptance probabilities for insert/delete moves and uses them to update biasing of the move.
MCMoveIDBiasAction(IntegratorMC, MCMoveInsertDeleteBiased, int, double, MCMoveOverlapListener, int) - Constructor for class etomica.integrator.mcmove.MCMoveIDBiasAction
MCMoveInsertDelete - Class in etomica.integrator.mcmove: Elementary Monte Carlo move in which a molecule of a specified species is inserted into or removed from a box.
MCMoveInsertDelete(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDelete
MCMoveInsertDeleteBiased - Class in etomica.integrator.mcmove: Biased MCMove for insertion and deletion.
MCMoveInsertDeleteBiased(IPotentialMaster, IRandom, ISpace, int, int) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
MCMoveInsertDeleteLatticeVacancy - Class in etomica.integrator.mcmove: Looks for atoms without a full set of first nearest neighbors and attempts insertions adjacent to one of those atoms.
MCMoveInsertDeleteLatticeVacancy(IPotentialMaster, IRandom, ISpace, IIntegrator, double, int, int) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce - Class in etomica.integrator.mcmove
MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr - Class in etomica.integrator.mcmove
MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell - Class in etomica.integrator.mcmove
MCMoveInsertDeleteVacancy - Class in etomica.integrator.mcmove: Looks for atoms without a full set of first nearest neighbors and attempts insertions adjacent to one of those atoms.
MCMoveInsertDeleteVacancy(IPotentialMaster, IRandom, ISpace, IIntegrator, double, int, int) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
mcMoveList - Variable in class etomica.integrator.mcmove.MCMoveManager
MCMoveManager - Class in etomica.integrator.mcmove
MCMoveManager(IRandom) - Constructor for class etomica.integrator.mcmove.MCMoveManager
MCMoveMolecular - Interface in etomica.integrator.mcmove: An interface that contains MoleculeIterator
MCMoveMolecule - Class in etomica.integrator.mcmove: Standard Monte Carlo molecule-displacement trial move.
MCMoveMolecule(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveMolecule
MCMoveMolecule(IPotentialMaster, IRandom, ISpace, double, double) - Constructor for class etomica.integrator.mcmove.MCMoveMolecule
mcMoveMolecule - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
mcMoveMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
mcMoveMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
MCMoveMoleculeCoupled - Class in etomica.normalmode: Standard Monte Carlo molecule-displacement trial move.
MCMoveMoleculeCoupled(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.normalmode.MCMoveMoleculeCoupled
MCMoveMoleculeCoupledDLPOLY - Class in etomica.paracetamol: Standard Monte Carlo molecule-displacement trial move.
MCMoveMoleculeCoupledDLPOLY(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
mcMoveMoleculeCoupledDLPOLY - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
mcMoveMoleculeCoupledDLPOLY - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
MCMoveMoleculeCoupledInitPert - Class in etomica.models.nitrogen: Standard Monte Carlo molecule-displacement trial move.
MCMoveMoleculeCoupledInitPert(IPotentialMaster, IRandom, ISpace, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
MCMoveMoleculeCoupledSuperBox - Class in etomica.models.nitrogen: Standard Monte Carlo molecule-displacement trial move for superbox.
MCMoveMoleculeCoupledSuperBox(IPotentialMaster, IRandom, ISpace, IBox, int, int, CoordinateDefinitionNitrogenSuperBox) - Constructor for class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
MCMoveMoleculeExchange - Class in etomica.integrator.mcmove: Performs a trial that results in the exchange of a molecule from one box to another.
MCMoveMoleculeExchange(IPotentialMaster, IRandom, ISpace, IntegratorBox, IntegratorBox) - Constructor for class etomica.integrator.mcmove.MCMoveMoleculeExchange
MCMoveMoleculeExchangeVLE - Class in etomica.modules.vle
MCMoveMoleculeExchangeVLE(IPotentialMaster, IRandom, ISpace, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.vle.MCMoveMoleculeExchangeVLE
mcMoveMoleculeMonomer - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
MCMoveMoleculeMonomer - Class in etomica.association: Monte Carlo molecule-displacement trial move for monomer molecules
MCMoveMoleculeMonomer(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveMoleculeMonomer
MCMoveMoleculeMonomer(IPotentialMaster, IRandom, ISpace, double, double) - Constructor for class etomica.association.MCMoveMoleculeMonomer
mcMoveMoleculeRotate - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
MCMoveMoleculeRotateAssociated - Class in etomica.association: Performs a rotation of a molecule that has an orientation coordinate.
MCMoveMoleculeRotateAssociated(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.association.MCMoveMoleculeRotateAssociated
mcMoveMoleculeSmer - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
MCMoveMoleculeSmer - Class in etomica.association: Monte Carlo molecule-displacement trial move for a molecule in smer
MCMoveMoleculeSmer(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveMoleculeSmer
MCMoveMoleculeSmer(IPotentialMaster, IRandom, ISpace, double, double) - Constructor for class etomica.association.MCMoveMoleculeSmer
mcMoveMulti - Variable in class etomica.virial.simulations.SimulationVirialPT
MCMoveMultiHarmonic - Class in etomica.gaussianwork: MCMove which moves all atoms.
MCMoveMultiHarmonic(P1Harmonic, IRandom) - Constructor for class etomica.gaussianwork.MCMoveMultiHarmonic
MCMoveMultiHarmonic - Class in etomica.modules.multiharmonic: MCMove which moves all atoms.
MCMoveMultiHarmonic(P1Harmonic, IRandom) - Constructor for class etomica.modules.multiharmonic.MCMoveMultiHarmonic
MCMoveOverlapListener - Class in etomica.integrator.mcmove
MCMoveOverlapListener(MCMoveInsertDeleteBiased, int, double, int, double) - Constructor for class etomica.integrator.mcmove.MCMoveOverlapListener
mcMoveOverlapMeter - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceAvgPressure
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceAvgPressure2
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceFE
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceFEHistogram
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceImposedFEFit
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceMuRoot
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceMuRoot1
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceMuRootPMatch
mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourcePMu
MCMovePhaseAngle - Class in etomica.normalmode
MCMovePhaseAngle(ISpace, NormalModesVariable, CoordinateDefinition, IRandom) - Constructor for class etomica.normalmode.MCMovePhaseAngle
MCMoveReptate - Class in etomica.models.hexane
MCMoveReptate(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.models.hexane.MCMoveReptate
MCMoveReptate(IPotentialMaster, IRandom, double, double, boolean, ISpace) - Constructor for class etomica.models.hexane.MCMoveReptate
mcMoveReptate - Variable in class etomica.virial.simulations.SimulationVirial
mcMoveRotate - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveRotate - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
mcMoveRotate - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
MCMoveRotate - Class in etomica.integrator.mcmove: Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
MCMoveRotate(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveRotate
mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirial
mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialOverlap
mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialPT
mcMoveRotate - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveRotateAssociated - Class in etomica.association: Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
MCMoveRotateAssociated(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.association.MCMoveRotateAssociated
mcMoveRotateMolecule - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
mcMoveRotateMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
mcMoveRotateMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
MCMoveRotateMolecule3D - Class in etomica.integrator.mcmove
MCMoveRotateMolecule3D(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveRotateMolecule3D
MCMoveRotateMolecule3DConstraint - Class in etomica.models.nitrogen: MCMoveRotate that moves the molecules according to pre-set constraint angle which is given by the parameter "angle" This class does not consider rotational energy, so the variable "energyChange" always returns zero getB() always returns positive one is to ensure the proposed move is always accepted
MCMoveRotateMolecule3DConstraint(IPotentialMaster, IRandom, ISpace, double, CoordinateDefinitionNitrogen, IBox) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
MCMoveRotateMolecule3DFixedAngle - Class in etomica.models.nitrogen: MCMoveRotate that moves the molecules according to pre-set constraint angle which is given by the parameter "angle" This class does not consider rotational energy, so the variable "energyChange" always returns zero getB() always returns positive one is to ensure the proposed move is always accepted the proposed angle criteria is based on u3 and u4 distribution
MCMoveRotateMolecule3DFixedAngle(IPotentialMaster, IRandom, ISpace, double, CoordinateDefinitionNitrogen, IBox) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
MCMoveRotateMolecule3DN2AveCosThetaConstraint - Class in etomica.models.nitrogen: Impose constraint to prevent the alpha-N2 phase from becoming orientationally-disordered the constraint imposed is the average cosine theta, where theta is the orientation angle off the molecular nominal orientation
MCMoveRotateMolecule3DN2AveCosThetaConstraint(IPotentialMaster, IRandom, ISpace, CoordinateDefinitionNitrogen, double) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
MCMoveRotateMolecule3DSuperBox - Class in etomica.models.nitrogen: MC Rotate Move 3D for superbox The potential master that being passed in this class is a "full-strength" potential without multiplying by 0.5 for the speciesA and speciesB interaction.
MCMoveRotateMolecule3DSuperBox(IPotentialMaster, IRandom, ISpace, int, int, CoordinateDefinitionNitrogenSuperBox) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
MCMoveRotateMoleculePhiTheta - Class in etomica.normalmode
MCMoveRotateMoleculePhiTheta(IPotentialMaster, IRandom, ISpace, IVectorMutable[], boolean) - Constructor for class etomica.normalmode.MCMoveRotateMoleculePhiTheta
MCMoveRotateNoSmer - Class in etomica.association
MCMoveRotateNoSmer(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.association.MCMoveRotateNoSmer
mcMoves() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
MCMoveSemigrand - Class in etomica.integrator.mcmove: Basic Monte Carlo move for semigrand-ensemble simulations.
MCMoveSemigrand(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveSemigrand
MCMoveSingleMode - Class in etomica.normalmode: A Monte Carlo move which selects each individual modes to move the atoms accordingly
MCMoveSingleMode(IPotentialMaster, IRandom) - Constructor for class etomica.normalmode.MCMoveSingleMode
MCMoveSmer - Class in etomica.association: Standard Monte Carlo atom-displacement trial move of Trimer
MCMoveSmer(ISimulation, PotentialMasterCell, ISpace, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmer
MCMoveSmer(PotentialMasterCell, IRandom, ISpace, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmer
mcMoveSmer - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveSmer - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
MCMoveSmerRotate - Class in etomica.association: Standard Monte Carlo atom-displacement trial move.
MCMoveSmerRotate(ISimulation, PotentialMasterCell, ISpace, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmerRotate
MCMoveSmerRotate(PotentialMasterCell, IRandom, ISpace, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmerRotate
mcMoveSmerRotate - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveSmerRotate - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
MCMoveSpinFlip - Class in etomica.spin: TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates
MCMoveSpinFlip(IPotentialMaster, IRandom) - Constructor for class etomica.spin.MCMoveSpinFlip
MCMoveStep - Class in etomica.integrator.mcmove
MCMoveStep(IPotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMoveStep
MCMoveStep(IPotentialMaster, MCMoveStepTracker) - Constructor for class etomica.integrator.mcmove.MCMoveStep
MCMoveStepDependent - Interface in etomica.integrator.mcmove
MCMoveStepTracker - Class in etomica.integrator.mcmove: This Class tracks acceptance statistics for an MCMove and also manages the move's step size.
MCMoveStepTracker() - Constructor for class etomica.integrator.mcmove.MCMoveStepTracker
mcMoveSwap - Variable in class etomica.freeenergy.npath.SimIdealGas
mcMoveSwap - Variable in class etomica.freeenergy.npath.SimLJ
MCMoveSwapCluster - Class in etomica.virial.paralleltempering: Swaps configurations and pairSet between boxes for a virial clustering simulation.
MCMoveSwapCluster(IntegratorMC, IntegratorMC, ISpace) - Constructor for class etomica.virial.paralleltempering.MCMoveSwapCluster
MCMoveSwapCluster.SwapFactory - Class in etomica.virial.paralleltempering
MCMoveSwapConfiguration - Class in etomica.integrator.mcmove: Basic MCMove for swapping coordinates of atoms in two boxes.
MCMoveSwapConfiguration(IntegratorBox, IntegratorBox, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveSwapConfiguration
MCMoveSwapConfiguration.SwapFactory - Class in etomica.integrator.mcmove
mcMoveTorsion - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
MCMoveTorsionAceticAcid - Class in etomica.integrator.mcmove: An MC Move for cluster simulations that performs torsion moves on acetic acid.
MCMoveTorsionAceticAcid(IPotentialMaster, ISpace, IRandom) - Constructor for class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
MCMoveTracker - Class in etomica.integrator.mcmove: This class is responsible for tracking acceptance statistics for an MCMove.
MCMoveTracker() - Constructor for class etomica.integrator.mcmove.MCMoveTracker
mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirial
mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirialOverlap
mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
MCMoveTrialCompletedEvent - Class in etomica.integrator.mcmove
MCMoveTrialCompletedEvent(MCMoveManager, boolean) - Constructor for class etomica.integrator.mcmove.MCMoveTrialCompletedEvent
MCMoveTrialFailedEvent - Class in etomica.integrator.mcmove: MC move event that indicates the move's trial failed, meaning that MCMove.doTrial() returned false.
MCMoveTrialFailedEvent(MCMoveManager) - Constructor for class etomica.integrator.mcmove.MCMoveTrialFailedEvent
MCMoveTrialInitiatedEvent - Class in etomica.integrator.mcmove
MCMoveTrialInitiatedEvent(MCMoveManager) - Constructor for class etomica.integrator.mcmove.MCMoveTrialInitiatedEvent
mcMoveVolume - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
mcMoveVolume - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
mcMoveVolume - Variable in class etomica.association.TestLJAssociationMC3D_NPT
mcMoveVolume - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
mcMoveVolume - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
MCMoveVolume - Class in etomica.integrator.mcmove: Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolume(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveVolume
MCMoveVolume(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.integrator.mcmove.MCMoveVolume
mcMoveVolume - Variable in class etomica.liquidLJ.LjMd3D
mcMoveVolume - Variable in class etomica.metastable.LJNPT
mcMoveVolume - Variable in class etomica.modules.ensembles.LJMC
mcMoveVolume - Variable in class etomica.normalmode.SimHSMDVacancy
mcMoveVolume - Variable in class etomica.normalmode.SimLJVacancy
mcMoveVolume - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
MCMoveVolumeAssociated - Class in etomica.association: Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeAssociated(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveVolumeAssociated
MCMoveVolumeAssociated(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.association.MCMoveVolumeAssociated
MCMoveVolumeAssociated.Agent - Class in etomica.association
MCMoveVolumeAssociatedMolecule - Class in etomica.association: Monte Carlo volume-change move for associating fluids simulations in the NPT ensemble.
MCMoveVolumeAssociatedMolecule(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.association.MCMoveVolumeAssociatedMolecule
MCMoveVolumeAssociatedMolecule(ISimulation, IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.association.MCMoveVolumeAssociatedMolecule
MCMoveVolumeAssociatedMolecule.Agent - Class in etomica.association
MCMoveVolumeExchange - Class in etomica.integrator.mcmove: Elementary Monte Carlo trial that exchanges volume between two boxs.
MCMoveVolumeExchange(IPotentialMaster, IRandom, ISpace, IntegratorBox, IntegratorBox) - Constructor for class etomica.integrator.mcmove.MCMoveVolumeExchange
MCMoveVolumeExchangeVLE - Class in etomica.modules.vle
MCMoveVolumeExchangeVLE(IPotentialMaster, IRandom, ISpace, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.vle.MCMoveVolumeExchangeVLE
MCMoveVolumeMonoclinic - Class in etomica.normalmode: Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeMonoclinic(IPotentialMaster, IRandom, ISpace) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinic
MCMoveVolumeMonoclinicAngle - Class in etomica.normalmode: Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeMonoclinicAngle(IPotentialMaster, IRandom, ISpace, IBox) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinicAngle
MCMoveVolumeMonoclinicScaled - Class in etomica.normalmode: Monte Carlo volume-change move for simulations of crystalline solids in the NPT ensemble (molecular model).
MCMoveVolumeMonoclinicScaled(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinicScaled
MCMoveVolumeMonoclinicScaled(IPotentialMaster, IRandom, ISpace, double, int) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinicScaled
MCMoveVolumeN2 - Class in etomica.models.nitrogen: Monte Carlo volume-change move for simulations in the NPT ensemble.
MCMoveVolumeN2(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.models.nitrogen.MCMoveVolumeN2
MCMoveVolumeN2(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.models.nitrogen.MCMoveVolumeN2
MCMoveVolumeSolid - Class in etomica.normalmode: Monte Carlo volume-change move for simulations of crystalline solids in the NPT ensemble.
MCMoveVolumeSolid(IPotentialMaster, CoordinateDefinition, IRandom, ISpace, double) - Constructor for class etomica.normalmode.MCMoveVolumeSolid
MCMoveVolumeSolidNPTMolecular - Class in etomica.normalmode: Monte Carlo volume-change move for simulations of crystalline solids in the NPT ensemble (molecular model).
MCMoveVolumeSolidNPTMolecular(IPotentialMaster, IRandom, ISpace, double) - Constructor for class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
MCMoveVolumeSolidNPTMolecular(IPotentialMaster, IRandom, ISpace, double, int) - Constructor for class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
MCMoveVolumeSolidNPTMolecularOriented - Class in etomica.normalmode: Class which handles orientation of linear molecules during volume change trials.
MCMoveVolumeSolidNPTMolecularOriented(IPotentialMaster, IRandom, ISpace, double, IVectorMutable[]) - Constructor for class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
mcMoveWiggle - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirial
mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap
mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
MCMoveWiggleAceticAcid - Class in etomica.integrator.mcmove: An MC Move for cluster simulations that "wiggles" for acetic acid.
MCMoveWiggleAceticAcid(ISimulation, IPotentialMaster, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
MCMoveWiggleAceticAcid(IPotentialMaster, IRandom, double, ISpace) - Constructor for class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
MCMoveWV - Class in etomica.normalmode
MCMoveWV(ISpace, NormalModesVariable, CoordinateDefinition, IRandom) - Constructor for class etomica.normalmode.MCMoveWV
mConnections - Variable in class etomica.virial.cluster.ClusterDiagram
MCParacetamolMonoclinicDLMULTI - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule using the potential model from DL_MULTI package with inclusion of multipole ewald-summation To get the lowest minimum configuration with MCMoveHarmonicStep Monoclinic Crystal The constructor takes in: 1.
MCParacetamolMonoclinicDLMULTI(Space, int, double, int, int[]) - Constructor for class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
MCParacetamolMonoclinicDLMULTIEquilibration - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule using the potential model from DL_MULTI package with inclusion of multipole ewald-summation Monoclinic Crystal
MCParacetamolMonoclinicDLMULTIEquilibration(Space) - Constructor for class etomica.paracetamol.MCParacetamolMonoclinicDLMULTIEquilibration
MCParacetamolMonoclinicDLMULTISimCalcS - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule using the potential model from DL_MULTI package with inclusion of multipole ewald-summation MC simulation of Paracetamol molecules in Form I (Monoclinic) with tabulation of the collective-coordinate S-matrix.
MCParacetamolMonoclinicDLMULTISimCalcS(Space) - Constructor for class etomica.paracetamol.MCParacetamolMonoclinicDLMULTISimCalcS
MCParacetamolOrthorhombicDLMULTI - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule using the potential model from DL_MULTI package with inclusion of multipole ewald-summation Orthorhombic Crystal * The constructor takes in: 1.
MCParacetamolOrthorhombicDLMULTI(Space, int, double, int, int[]) - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
MCParacetamolOrthorhombicDLMULTIEquilibration - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule using the potential model from DL_MULTI package with inclusion of multipole ewald-summation To get the lowest minimum cofiguration with MCMoveHarmonicStep Orthorhombic Crystal
MCParacetamolOrthorhombicDLMULTIEquilibration(Space) - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTIEquilibration
MCParacetamolOrthorhombicDLMULTISimCalcS - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule using the potential model from DL_MULTI package with inclusion of multipole ewald-summation MC simulation of Paracetamol molecules in Form II (Orthorhombic) with tabulation of the collective-coordinate S-matrix.
MCParacetamolOrthorhombicMoveHarmonic - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule Orthorhombic Crystal
MCParacetamolOrthorhombicMoveHarmonic() - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
MCParacetamolOrthorhombicMoveHarmonicStep - Class in etomica.paracetamol: Three-dimensional soft-sphere MC simulation for paracetamol molecule Orthorhombic Crystal
MCParacetamolOrthorhombicMoveHarmonicStep() - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
MCSIMULATION - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
MCSIMULATION - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
mcSteps - Variable in class etomica.integrator.IntegratorMD
mcSteps - Variable in class etomica.interfacial.LJMD.LJMDParams
MDParacetamolMonoclinic - Class in etomica.paracetamol: Three-dimensional soft-sphere molecular dynamics simulation for paracetamol molecule, using neighbor listing.
MDParacetamolOrthorhombic - Class in etomica.paracetamol: Three-dimensional soft-sphere molecular dynamics simulation for paracetamol molecule, using neighbor listing.
ME(IVector) - Method in interface etomica.api.IVectorMutable: Minus-equals (-=) operation.
ME(IData) - Method in interface etomica.data.IData: Minus-equals (-=) operation.
ME(IData) - Method in class etomica.data.types.DataDouble: Minus-equals (-=) operation.
ME(IData) - Method in class etomica.data.types.DataDoubleArray: Minus-equals (-=) operation.
ME(IData) - Method in class etomica.data.types.DataDoubleBDArray: Minus-equals (-=) operation.
ME(IData) - Method in class etomica.data.types.DataGroup
ME(IData) - Method in class etomica.data.types.DataTensor: Minus-equals (-=) operation.
ME(IData) - Method in class etomica.data.types.DataVector: Minus-equals (-=) operation.
ME(Tensor) - Method in interface etomica.space.Tensor
ME(Tensor) - Method in class etomica.space1d.Tensor1D
ME(IVector) - Method in class etomica.space1d.Vector1D
ME(Tensor) - Method in class etomica.space2d.Tensor2D
ME(IVector) - Method in class etomica.space2d.Vector2D
ME(Tensor) - Method in class etomica.space3d.Tensor3D
ME(IVector) - Method in class etomica.space3d.Vector3D
ME(Tensor) - Method in class etomica.spaceNd.TensorND
ME(IVector) - Method in class etomica.spaceNd.VectorND
MEAM_3DMDwithGB - Class in etomica.meam: Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method (MEAM) Potential.
MEAM_3DMDwithGB() - Constructor for class etomica.meam.MEAM_3DMDwithGB
MEAM_3DMDwithSnAgGB - Class in etomica.meam: Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method (MEAM) Potential.
MEAM_3DMDwithSnAgGB() - Constructor for class etomica.meam.MEAM_3DMDwithSnAgGB
MEAM_3DMDwithSnCuGB - Class in etomica.meam: Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method (MEAM) Potential.
MEAM_3DMDwithSnCuGB() - Constructor for class etomica.meam.MEAM_3DMDwithSnCuGB
MEAM_MC - Class in etomica.meam
MEAM_MC() - Constructor for class etomica.meam.MEAM_MC
MEAMMd3D - Class in etomica.meam: Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method (MEAM) Potential.
MEAMMd3D() - Constructor for class etomica.meam.MEAMMd3D
MEAMMd3DforCluster - Class in etomica.meam: Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method (MEAM) Potential.
MEAMMd3DforCluster() - Constructor for class etomica.meam.MEAMMd3DforCluster
MEAMMd3DThreaded - Class in etomica.threaded.domain: Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method (MEAM) Potential.
MEAMMd3DThreaded(int, int) - Constructor for class etomica.threaded.domain.MEAMMd3DThreaded
MEAMMd3DThreadedforCluster - Class in etomica.threaded.domain
MEAMMd3DThreadedforCluster() - Constructor for class etomica.threaded.domain.MEAMMd3DThreadedforCluster
measure - Static variable in class org.jmol.script.Token
Measure - Class in org.jmol.util
Measure() - Constructor for class org.jmol.util.Measure
MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
measureallmodels - Static variable in class org.jmol.script.Token
measurementlabels - Static variable in class org.jmol.script.Token
measurements - Static variable in class org.jmol.script.Token
measurementunits - Static variable in class org.jmol.script.Token
mediaType - Variable in class etomica.graph.view.rasterizer.SVGConverter: Media type for which the SVG image should be rendered
MEGA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺⁶.
membraneDim - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
membraneDim - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
membraneThicknessPerLayer - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
membraneThicknessSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
membraneThicknessSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
membraneTotalThickness - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
membraneWidth - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
membraneWidth - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
membraneWidthSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
mERBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
mergeData(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
mergeData(Map<IntSet, MeterVirialBinMultiThreaded.MyData>) - Method in class etomica.virial.MeterVirialBinMultiThreaded
mergeData(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
MersenneTwister - Class in etomica.util: Mersenne Twister and MersenneTwisterFast:
MersenneTwister() - Constructor for class etomica.util.MersenneTwister: Constructor using the default seed.
MersenneTwister(long) - Constructor for class etomica.util.MersenneTwister: Constructor using a given seed.
MersenneTwisterFast - Class in etomica.util: Mersenne Twister and MersenneTwisterFast:
MersenneTwisterFast() - Constructor for class etomica.util.MersenneTwisterFast: Constructor using the default seed.
MersenneTwisterFast(long) - Constructor for class etomica.util.MersenneTwisterFast: Constructor using a given seed.
mesh - Static variable in class org.jmol.script.Token
meshRibbon - Static variable in class org.jmol.script.Token
meshscale - Static variable in class org.jmol.script.Token
MeshSurface - Class in org.jmol.util
MeshSurface() - Constructor for class org.jmol.util.MeshSurface
meshType - Variable in class org.jmol.util.MeshSurface
MESSAGE_ABOUT_TO_TRANSCODE - Static variable in class etomica.graph.view.rasterizer.Main
MESSAGE_ABOUT_TO_TRANSCODE_SOURCE - Static variable in class etomica.graph.view.rasterizer.Main
MESSAGE_CONVERSION_FAILED - Static variable in class etomica.graph.view.rasterizer.Main
MESSAGE_CONVERSION_SUCCESS - Static variable in class etomica.graph.view.rasterizer.Main
Messages - Class in etomica.graph.view.rasterizer: This class manages the message for the bridge module.
Messages() - Constructor for class etomica.graph.view.rasterizer.Messages: This class does not need to be instantiated.
messagestylechime - Static variable in class org.jmol.script.Token
Metadata - Interface in etomica.graph.model
metaDataComparator - Static variable in class etomica.graph.model.impl.MetadataImpl
MetadataImpl - Class in etomica.graph.model.impl
MetadataImpl(char, char) - Constructor for class etomica.graph.model.impl.MetadataImpl
meter - Variable in class etomica.data.meter.MeterProfile: Meter that defines the property being profiled.
meter - Variable in class etomica.data.meter.MeterProfileByAtoms: Meter that defines the property being profiled.
meter - Variable in class etomica.data.meter.MeterProfileByVolume: Meter that defines the property being profiled.
meter - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
meter - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
meter - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
meter - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
meter - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
meter - Variable in class etomica.modules.droplet.AtomFilterLiquid
meter - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
meter - Variable in class etomica.normalmode.HTTPSoftSphereApplet
meter - Variable in class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
meter - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
meter - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
meter - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
meter - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
meter - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
meter - Variable in class etomica.spin.Heisenberg
Meter - Class in etomica.units: The meter unit of length, equal to 10^10 angstroms.
meter - Variable in class etomica.virial.simulations.SimulationVirial
meter - Variable in class etomica.virial.simulations.SimulationVirialPT
meter - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
meter - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
meterA - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
meterA - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
meterA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
meterAccept - Variable in class etomica.virial.simulations.SimulationVirialPT
meterAcceptP - Variable in class etomica.virial.simulations.SimulationVirialPT
MeterAPIPotentialEnergy - Class in etomica.normalmode: Meter that returns the potential energy using an IAPIPotential.
MeterAPIPotentialEnergy(IAPIPotential) - Constructor for class etomica.normalmode.MeterAPIPotentialEnergy
MeterAtomicDisplacement - Class in etomica.normalmode: Calculates the average atomic displacement from their lattice sites
MeterAtomicDisplacement(ISpace, CoordinateDefinition) - Constructor for class etomica.normalmode.MeterAtomicDisplacement
MeterAvgBondLength - Class in etomica.data.meter
MeterAvgBondLength() - Constructor for class etomica.data.meter.MeterAvgBondLength
meterB - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
meterB - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
meterB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
MeterBoltzmann - Class in etomica.models.nitrogen: Meter used for overlap sampling in the target-sampled system.
MeterBoltzmann(IntegratorBox, MeterPotentialEnergy) - Constructor for class etomica.models.nitrogen.MeterBoltzmann
MeterBoltzmann - Class in etomica.normalmode: Meter used for overlap sampling in the target-sampled system.
MeterBoltzmann(IntegratorBox, MeterPotentialEnergy, double, double) - Constructor for class etomica.normalmode.MeterBoltzmann
MeterBoltzmannA - Class in etomica.gaussianwork: Multiharmonic system Meter used for overlap sampling in the A-sampled system.
MeterBoltzmannA(IntegratorBox, PotentialMaster) - Constructor for class etomica.gaussianwork.MeterBoltzmannA
MeterBoltzmannB - Class in etomica.gaussianwork: Multiharmonic system Meter used for overlap sampling in the B-sampled system.
MeterBoltzmannB(IntegratorBox, PotentialMaster) - Constructor for class etomica.gaussianwork.MeterBoltzmannB
MeterBoltzmannDirect - Class in etomica.models.nitrogen: Meter used for overlap sampling in the target-sampled system.
MeterBoltzmannDirect(IntegratorBox, MeterPotentialEnergy) - Constructor for class etomica.models.nitrogen.MeterBoltzmannDirect
MeterBoltzmannHarmonic - Class in etomica.normalmode: Meter used for overlap sampling in the harmonic-sampled system.
MeterBoltzmannHarmonic(MCMoveHarmonic, PotentialMaster) - Constructor for class etomica.normalmode.MeterBoltzmannHarmonic
MeterBoltzmannHTTP - Class in etomica.normalmode: Same as TargetTP class but is used by MethodBoltzmannHTTP It is to illustrate the idea of HTTP method.
MeterBoltzmannHTTP(IPotentialMaster, ISpecies, ISpace, ISimulation) - Constructor for class etomica.normalmode.MeterBoltzmannHTTP
MeterBoltzmannRotPerturb - Class in etomica.models.nitrogen: Meter used for overlap sampling in the target-sampled system.
MeterBoltzmannRotPerturb(IntegratorMC, IPotentialMaster, ISpecies, ISpace, ISimulation, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterBoltzmannRotPerturb
MeterBoltzmannTarget - Class in etomica.normalmode: Meter used for overlap sampling in the target-sampled system.
MeterBoltzmannTarget(DataSourceScalar, DataSourceScalar) - Constructor for class etomica.normalmode.MeterBoltzmannTarget
MeterBondOrderParameterQ - Class in etomica.data.meter: The Bond Order Parameter Ql provides a metric that indicates the crystallinity of a box.
MeterBondOrderParameterQ(ISpace) - Constructor for class etomica.data.meter.MeterBondOrderParameterQ
MeterBondOrderParameterQ(ISpace, double) - Constructor for class etomica.data.meter.MeterBondOrderParameterQ
MeterChainLength - Class in etomica.modules.chainequilibrium
MeterChainLength(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.MeterChainLength
MeterChainLength.AtomTag - Class in etomica.modules.chainequilibrium
MeterCompareMultipleWVBrute - Class in etomica.models.oneDHardRods: Meter which measures a hard rod energy plus a harmonic energy of a system The harmonic energy is determined by removing the effects of some normal mode coordinates, and applying 1/2 omega^2 nmc^2 to them.
MeterCompareMultipleWVBrute(IPotentialMaster, CoordinateDefinition, IBox) - Constructor for class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
MeterCompareMultipleWVBrute(String, IPotentialMaster, CoordinateDefinition, IBox) - Constructor for class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
MeterCompareWVShortcut - Class in etomica.models.oneDHardRods: This meter assumes the use of only MCMoveCompareMode in the simulation.
MeterCompareWVShortcut(IPotentialMaster, MCMoveCompareMultipleWV) - Constructor for class etomica.models.oneDHardRods.MeterCompareWVShortcut
MeterConversion - Class in etomica.modules.chainequilibrium: Meter for the reaction conversion (fraction of reacted sites).
MeterConversion(IBox, AtomLeafAgentManager) - Constructor for class etomica.modules.chainequilibrium.MeterConversion
meterCountAtoms - Variable in class etomica.modules.adsorption.ModifierPMu
meterCycles - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
meterCycles - Variable in class etomica.simulation.prototypes.HsMc2d
meterCycles - Variable in class etomica.simulation.prototypes.SoftSphere3d
MeterDADB - Class in etomica.normalmode
MeterDADB(ISpace, DataSourceScalar, PotentialMaster, CoordinateDefinition, double) - Constructor for class etomica.normalmode.MeterDADB
MeterDDP - Class in etomica.normalmode: Meter that measures the overlap averages for perturbing from a solid at one density into other densities.
MeterDDP(IPotentialMaster, ISpecies, ISpace, ISimulation) - Constructor for class etomica.normalmode.MeterDDP
meterDeformation - Variable in class etomica.modules.droplet.Droplet
MeterDeformation - Class in etomica.modules.droplet
MeterDeformation(ISpace) - Constructor for class etomica.modules.droplet.MeterDeformation
MeterDensity - Class in etomica.data.meter: Meter for measurement of the total molecule number density in a box Molecule number density is defined (number of molecules)/(volume of box)
MeterDensity(ISpace) - Constructor for class etomica.data.meter.MeterDensity
meterDensity - Variable in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
meterDensity - Variable in class etomica.modules.vle.MCMoveVolumeExchangeVLE
MeterDensityCO - Class in etomica.modules.catalysis
MeterDensityCO(IBox, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityCO
MeterDensityCO2 - Class in etomica.modules.catalysis
MeterDensityCO2(IBox, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityCO2
MeterDensityDistribution - Class in etomica.metastable
MeterDensityDistribution(ISpace, IBox, int) - Constructor for class etomica.metastable.MeterDensityDistribution
MeterDensityO2 - Class in etomica.modules.catalysis
MeterDensityO2(IBox, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityO2
MeterDensitySides - Class in etomica.modules.mu
MeterDensitySides(IBox, ISpecies, boolean) - Constructor for class etomica.modules.mu.MeterDensitySides
MeterDifferentImageAdd - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterDifferentImageAdd(ISimulation, ISpace, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAdd
MeterDifferentImageAdd(ISimulation, ISpace, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAdd
MeterDifferentImageAdd1D - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterDifferentImageAdd1D(String, int, double, Simulation, Primitive, Basis, CoordinateDefinition, NormalModes, double) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
MeterDifferentImageAddDoubleSize - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterDifferentImageAddDoubleSize(ISimulation, ISpace, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAddDoubleSize
MeterDifferentImageAddDoubleSize(ISimulation, ISpace, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAddDoubleSize
MeterDifferentImageSubtract - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterDifferentImageSubtract(ISimulation, ISpace, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtract
MeterDifferentImageSubtract(ISimulation, ISpace, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtract
MeterDifferentImageSubtract1D - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterDifferentImageSubtract1D(String, int, double, Simulation, Primitive, Basis, CoordinateDefinition, NormalModes, double) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
MeterDifferentImageSubtractDoubleSize - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterDifferentImageSubtractDoubleSize(ISimulation, ISpace, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtractDoubleSize
MeterDifferentImageSubtractDoubleSize(ISimulation, ISpace, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtractDoubleSize
MeterDihedralAngle - Class in etomica.data.meter: Meter for tabulation of a dihedral angle distribution between nearest neighbors.
MeterDihedralAngle(ISpace) - Constructor for class etomica.data.meter.MeterDihedralAngle: Creates meter with default to compute dihedral angle for all leaf atoms in a box.
MeterDimerFraction - Class in etomica.modules.reactionequilibrium
MeterDimerFraction(AtomLeafAgentManager) - Constructor for class etomica.modules.reactionequilibrium.MeterDimerFraction
meterDimerFraction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
MeterDimerMoleFraction - Class in etomica.association: Meter for measurement of species mole fraction within a specified subvolume
MeterDimerMoleFraction(ISpace, IBox) - Constructor for class etomica.association.MeterDimerMoleFraction
MeterDipoleSumSquared1site - Class in etomica.data.meter: meter for (sum dipole)^2, used for dielectric constant calculation
MeterDipoleSumSquared1site(ISpace, IBox, double) - Constructor for class etomica.data.meter.MeterDipoleSumSquared1site
MeterDipoleSumSquaredMappedAverage - Class in etomica.data.meter: meter for AEE use mapping average
MeterDipoleSumSquaredMappedAverage(ISpace, IBox, ISimulation, double, double, IPotentialMaster) - Constructor for class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
MeterDipoleSumSquaredTIP4PWater - Class in etomica.data.meter: meter for (sum dipole)^2 used for dielectric constant calculation
MeterDipoleSumSquaredTIP4PWater(ISpace, IBox) - Constructor for class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
MeterDirectInitPert - Class in etomica.models.nitrogen: Meter used for overlap sampling in the target-sampled system.
MeterDirectInitPert(IntegratorBox, MeterPotentialEnergy, CoordinateDefinitionNitrogen, IRandom) - Constructor for class etomica.models.nitrogen.MeterDirectInitPert
MeterDirectSamplingHarmonic - Class in etomica.normalmode: Meter used for overlap sampling in the harmonic-sampled system.
MeterDirectSamplingHarmonic(MCMoveHarmonic, PotentialMaster) - Constructor for class etomica.normalmode.MeterDirectSamplingHarmonic
MeterDirectSamplingTarget - Class in etomica.normalmode: Meter used for overlap sampling in the target-sampled system.
MeterDirectSamplingTarget(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterDirectSamplingTarget
MeterDisplacementMoleculeRMS - Class in etomica.normalmode
MeterDisplacementMoleculeRMS(ISpace, CoordinateDefinitionMolecule) - Constructor for class etomica.normalmode.MeterDisplacementMoleculeRMS
MeterDisplacementRMS - Class in etomica.normalmode
MeterDisplacementRMS(ISpace, CoordinateDefinition) - Constructor for class etomica.normalmode.MeterDisplacementRMS
MeterDP - Class in etomica.normalmode: Meter that measures the overlap averages for perturbing from a solid at one density into other densities.
MeterDP(IPotentialMaster, ISpecies, ISpace, ISimulation) - Constructor for class etomica.normalmode.MeterDP
meterE2E - Variable in class etomica.modules.colloid.ColloidGraphic
MeterElongation - Class in etomica.modules.materialfracture
MeterElongation() - Constructor for class etomica.modules.materialfracture.MeterElongation
MeterEnd2End - Class in etomica.modules.colloid: Measures the end-to-end squared distance for the colloid system, averaged across the grafted chains.
MeterEnd2End(ISpace) - Constructor for class etomica.modules.colloid.MeterEnd2End
MeterEndToEnd - Class in etomica.modules.rheology: Meter that measures that end to end distance of the molecules
MeterEndToEnd(ISpace) - Constructor for class etomica.modules.rheology.MeterEndToEnd
meterEnergy - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
meterEnergy - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
MeterEnergy - Class in etomica.data.meter: Meter for measurement of the total (potential and kinetic) energy in a box This meter is constructed from kinetic-energy and a potential-energy meters An instance of this meter is placed in each box to allow for energy measurements in the box
MeterEnergy(IPotentialMaster, IBox) - Constructor for class etomica.data.meter.MeterEnergy
meterEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmann
meterEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmannDirect
meterEnergy - Variable in class etomica.models.nitrogen.MeterDirectInitPert
meterEnergy - Variable in class etomica.normalmode.MeterBoltzmann
meterEnergy - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
meterEnergy - Variable in class etomica.normalmode.MeterBoltzmannTarget
meterEnergy - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
meterEnergy - Variable in class etomica.normalmode.MeterDirectSamplingTarget
meterEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
meterEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
meterEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
meterEnergy - Variable in class etomica.normalmode.MeterWorkTargetBennet
meterEnergy - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
meterEnergy - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
meterEnergy - Variable in class etomica.normalmode.SimUmbrella
meterEnergy - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
meterEnergy - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
meterEnergyA - Variable in class etomica.gaussianwork.MeterBoltzmannA
meterEnergyA - Variable in class etomica.gaussianwork.MeterBoltzmannB
meterEnergyB - Variable in class etomica.gaussianwork.MeterBoltzmannA
meterEnergyB - Variable in class etomica.gaussianwork.MeterBoltzmannB
MeterEnthalpy(IntegratorGear4NPH, int) - Constructor for class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
MeterEntropy - Class in etomica.modules.entropylottery: Calculates the entropy of the distribution of Atoms in a Box using Stirling's approximation.
MeterEntropy() - Constructor for class etomica.modules.entropylottery.MeterEntropy
MeterExcessAdsorbed - Class in etomica.modules.adsorption
MeterExcessAdsorbed(ISpecies, EOSSW) - Constructor for class etomica.modules.adsorption.MeterExcessAdsorbed
MeterF - Class in etomica.models.oneDHardRods
MeterF(CoordinateDefinition) - Constructor for class etomica.models.oneDHardRods.MeterF
MeterFlux - Class in etomica.modules.dcvgcmd
MeterFlux(MyMCMove, IntegratorDCVGCMD) - Constructor for class etomica.modules.dcvgcmd.MeterFlux
MeterFlux - Class in etomica.modules.rosmosis: Meter to measure flux across a boundary or boundaries.
MeterFlux(ISimulation, ISpace) - Constructor for class etomica.modules.rosmosis.MeterFlux
meterFlux0 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
meterFlux1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
meterFlux2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
meterFlux3 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
MeterFreeEnergy - Class in etomica.modules.multiharmonic: Computes the free-enery difference through free-energy perturbation.
MeterFreeEnergy(P1Harmonic, P1Harmonic) - Constructor for class etomica.modules.multiharmonic.MeterFreeEnergy
meterHarm - Variable in class etomica.models.clathrates.MinimizationTIP4P
meterHarm - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
meterHarmonic - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
meterHarmonic - Variable in class etomica.normalmode.MeterWorkBennetTarget
meterHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
meterHarmonic - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
MeterHarmonicCoordinate - Class in etomica.normalmode
MeterHarmonicCoordinate(CoordinateDefinition) - Constructor for class etomica.normalmode.MeterHarmonicCoordinate
meterHarmonicCoordinate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
meterHarmonicEnergy - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
meterHarmonicEnergy - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
meterHarmonicEnergy - Variable in class etomica.normalmode.MeterDirectSamplingTarget
MeterHarmonicEnergy - Class in etomica.normalmode: Meter that calculates the harmonic energy of a configuration given eigenvectors and omegas corresponding to wave vectors.
MeterHarmonicEnergy(CoordinateDefinition, NormalModes) - Constructor for class etomica.normalmode.MeterHarmonicEnergy
meterHarmonicEnergy - Variable in class etomica.normalmode.MeterWorkTargetBennet
meterHarmonicEnergy - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
meterHarmonicEnergy - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
meterHarmonicEnergy - Variable in class etomica.normalmode.SimBennet
meterHarmonicEnergy - Variable in class etomica.normalmode.SimHarmonicUmbrella
meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlap
meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphere
meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSSnxy
meterHarmonicEnergy - Variable in class etomica.normalmode.SimTargetUmbrella
meterHarmonicEnergy - Variable in class etomica.normalmode.SimUmbrella
meterHarmonicEnergy - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
MeterHarmonicEnergyFromMove - Class in etomica.normalmode: Meter that returns the harmonic energy from the MC move as a data source.
MeterHarmonicEnergyFromMove(MCMoveHarmonic) - Constructor for class etomica.normalmode.MeterHarmonicEnergyFromMove
MeterHarmonicSingleEnergy - Class in etomica.normalmode: Meter that calculates the Boltzmann-factored harmonic energy of each normal mode for a configuration given eigenvectors and omegas corresponding to wave vectors.
MeterHarmonicSingleEnergy(CoordinateDefinition, NormalModes) - Constructor for class etomica.normalmode.MeterHarmonicSingleEnergy
MeterHyperVirial - Class in etomica.data.meter: Meter for measurement of the hypervirial, r^2 d2u/dr2 + r du/dr
MeterHyperVirial() - Constructor for class etomica.data.meter.MeterHyperVirial
MeterHyperVirial(ISpace, boolean) - Constructor for class etomica.data.meter.MeterHyperVirial: If full is true, then the pressure is also calculated and three values are returned.
meterJacobian - Variable in class etomica.normalmode.MCMovePhaseAngle
meterJacobian - Variable in class etomica.normalmode.MCMoveWV
MeterJacobian - Class in etomica.normalmode
MeterJacobian(CoordinateDefinition, NormalModesVariable) - Constructor for class etomica.normalmode.MeterJacobian
meterKE - Variable in class etomica.data.meter.MeterTemperature
meterKE - Variable in class etomica.integrator.IntegratorMD
MeterKineticEnergy - Class in etomica.data.meter: Meter for the total kinetic energy in a box Computes total KE by summing values of KE returned by every atom in the box.
MeterKineticEnergy() - Constructor for class etomica.data.meter.MeterKineticEnergy
MeterKineticEnergyFromIntegrator - Class in etomica.data.meter: Acts as a DataSource to retrieve the energy from the integrator
MeterKineticEnergyFromIntegrator() - Constructor for class etomica.data.meter.MeterKineticEnergyFromIntegrator
MeterKineticEnergyFromIntegrator(IntegratorMD) - Constructor for class etomica.data.meter.MeterKineticEnergyFromIntegrator
MeterKineticEnergyRigid - Class in etomica.data.meter: Meter for the total kinetic energy in a box Computes total KE by summing values of KE returned by every atom in the box.
MeterKineticEnergyRigid(ISpace, ISimulation) - Constructor for class etomica.data.meter.MeterKineticEnergyRigid
MeterKineticEnergyRigid(ISpace, ISimulation, IBox) - Constructor for class etomica.data.meter.MeterKineticEnergyRigid
MeterLoad - Class in etomica.modules.materialfracture: Meter that calculates the stress within the gage cell.
MeterLoad(PotentialCalculationForceStress) - Constructor for class etomica.modules.materialfracture.MeterLoad
MeterLocalDensity - Class in etomica.data.meter: Meter for measurement of density within a specified subvolume
MeterLocalDensity(IBox) - Constructor for class etomica.data.meter.MeterLocalDensity
MeterLocalMoleFraction - Class in etomica.data.meter: Meter for measurement of species mole fraction within a specified subvolume
MeterLocalMoleFraction(ISpace, IBox) - Constructor for class etomica.data.meter.MeterLocalMoleFraction
MeterMappedU - Class in etomica.mappedvirial
MeterMappedU(ISpace, IPotentialMaster, IBox, int) - Constructor for class etomica.mappedvirial.MeterMappedU
MeterMappedVirial - Class in etomica.mappedvirial
MeterMappedVirial(ISpace, IPotentialMaster, IBox, int) - Constructor for class etomica.mappedvirial.MeterMappedVirial
MeterMappedVirialV - Class in etomica.mappedvirial
MeterMappedVirialV(ISpace, IPotentialMaster, IBox, int) - Constructor for class etomica.mappedvirial.MeterMappedVirialV
MeterMaxExpansion - Class in etomica.normalmode: measures the maximum amount by which by which the HS diameter could increase without causing overlap
MeterMaxExpansion(ISpace, IBox, NeighborListManager) - Constructor for class etomica.normalmode.MeterMaxExpansion
MeterMBAR - Class in etomica.modules.multiharmonic.mbar
MeterMBAR(DataSourceScalar[], double) - Constructor for class etomica.modules.multiharmonic.mbar.MeterMBAR
MeterMeanForce - Class in etomica.mappedvirial
MeterMeanForce(ISpace, IPotentialMaster, Potential2SoftSpherical, IBox, int) - Constructor for class etomica.mappedvirial.MeterMeanForce
MeterMeanSquareDisplacement - Class in etomica.data.meter: Computes the mean square displacement for a set of atoms.
MeterMeanSquareDisplacement(ISpace, IntegratorBox) - Constructor for class etomica.data.meter.MeterMeanSquareDisplacement
MeterMeanSquareDisplacement(ISpace, IntegratorBox, AtomIteratorBoxDependent) - Constructor for class etomica.data.meter.MeterMeanSquareDisplacement
MeterMoleFraction - Class in etomica.data.meter: Meter for measurement of the species mole fraction in a box.
MeterMoleFraction() - Constructor for class etomica.data.meter.MeterMoleFraction
MeterMomentumCOM - Class in etomica.data.meter: Returns the instantaneous total center-of-mass momentum, summed over all leaf atoms in a box.
MeterMomentumCOM(ISpace) - Constructor for class etomica.data.meter.MeterMomentumCOM
MeterNMCBaskets - Class in etomica.models.oneDHardRods
MeterNMCBaskets(CoordinateDefinition, IVectorMutable[], int) - Constructor for class etomica.models.oneDHardRods.MeterNMCBaskets
MeterNMCBaskets(CoordinateDefinition, IVectorMutable[], int, boolean) - Constructor for class etomica.models.oneDHardRods.MeterNMCBaskets
MeterNMolecules - Class in etomica.data.meter: Meter for recording the total number of molecules in the box
MeterNMolecules() - Constructor for class etomica.data.meter.MeterNMolecules
MeterNormalizedCoord - Class in etomica.models.nitrogen: Sample the distribution of the normalized coordinate for the atoms/ molecules from coordinate definition, calcU method.
MeterNormalizedCoord(IBox, CoordinateDefinition, ISpecies) - Constructor for class etomica.models.nitrogen.MeterNormalizedCoord
MeterNormalizedCoord(IBox, CoordinateDefinition, ISpecies, boolean) - Constructor for class etomica.models.nitrogen.MeterNormalizedCoord
MeterNormalizedCoordBeta - Class in etomica.models.nitrogen: Sample the distribution of the normalized coordinate for the atoms/ molecules from coordinate definition, calcU method.
MeterNormalizedCoordBeta(IBox, CoordinateDefinition, ISpecies) - Constructor for class etomica.models.nitrogen.MeterNormalizedCoordBeta
MeterNormalMode - Class in etomica.normalmode: Calculates the S-matrix for a configuration.
MeterNormalMode() - Constructor for class etomica.normalmode.MeterNormalMode
meterNormalMode - Variable in class etomica.normalmode.WriteS
MeterNormalModeCoordinate - Class in etomica.models.oneDHardRods: Class which calculates all of the normal mode coordinates for a system.
MeterNormalModeCoordinate(CoordinateDefinition, IVectorMutable[]) - Constructor for class etomica.models.oneDHardRods.MeterNormalModeCoordinate
MeterNormalStress - Class in etomica.modules.rheology: Meter to measure normal stress of a polymer in a shear field.
MeterNormalStress(ISpace) - Constructor for class etomica.modules.rheology.MeterNormalStress
MeterOrientation - Class in etomica.modules.interfacial: Meter for collecting the molecular orientation of the dimer.
MeterOrientation(ISpace) - Constructor for class etomica.modules.interfacial.MeterOrientation
MeterOrientationDistribution - Class in etomica.models.nitrogen: Meter that measures the spherical coordinate angles angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane) and x-axis angle[1]: is phi, angle between the molecular axis vector and z-axis
MeterOrientationDistribution(IBox, CoordinateDefinitionNitrogen, ISpecies) - Constructor for class etomica.models.nitrogen.MeterOrientationDistribution
MeterOrientationOrderParameter - Class in etomica.models.nitrogen: Meter used to sample orientation order parameter
MeterOrientationOrderParameter(CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterOrientationOrderParameter
MeterOsmoticPressure - Class in etomica.modules.osmosis: Osmotic pressure meter that calculates the difference in
MeterOsmoticPressure(ISpace, P1HardBoundary[]) - Constructor for class etomica.modules.osmosis.MeterOsmoticPressure
MeterOsmoticPressure - Class in etomica.modules.rosmosis: Meter to measure flux across a boundary or boundaries.
MeterOsmoticPressure(IPotentialCalculationWallForce, IBox) - Constructor for class etomica.modules.rosmosis.MeterOsmoticPressure
MeterOverlap - Class in etomica.models.oneDHardRods
MeterOverlap(String, Dimension, DataSourceScalar, DataSourceScalar, double) - Constructor for class etomica.models.oneDHardRods.MeterOverlap: Put the system you are measuring in as the first DataSourceScalar
MeterOverlap - Class in etomica.overlap
MeterOverlap(IEtomicaDataSource, IEtomicaDataSource, double, boolean) - Constructor for class etomica.overlap.MeterOverlap: Meter to measure the "overlap" function for free energy calculations, used as input to an AccumulatorVirialOverlapSingleAverage.
meterOverlapA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
meterOverlapA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
meterOverlapB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
meterOverlapB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
MeterOverlapSameGaussian - Class in etomica.models.oneDHardRods
MeterOverlapSameGaussian(String, Dimension, DataSourceScalar, DataSourceScalar, double) - Constructor for class etomica.models.oneDHardRods.MeterOverlapSameGaussian: Put the system you are measuring in as the first DataSourceScalar
MeterOverlapSameGaussian1D - Class in etomica.models.oneDHardRods
MeterOverlapSameGaussian1D(String, Dimension, DataSourceScalar, DataSourceScalar, double) - Constructor for class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D: Put the system you are measuring in as the first DataSourceScalar
MeterOverlapSwitch - Class in etomica.normalmode: Meter whose purpose in life is to measure the overlap between systems defined by a combination of two energy meters.
MeterOverlapSwitch(IPotentialMaster, IPotentialMaster) - Constructor for class etomica.normalmode.MeterOverlapSwitch
meterPE - Variable in class etomica.integrator.IntegratorBox
meterPE - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
meterPE - Variable in class etomica.models.clathrates.MinimizationTIP4P
meterPE - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
meterPE - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
meterPE - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
meterPE - Static variable in class etomica.models.rowley.DimerApproach
meterPE - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
meterPE - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
meterPE - Variable in class etomica.normalmode.MeterDADB
meterPE - Variable in class etomica.normalmode.MeterSolidProps
meterPE - Variable in class etomica.normalmode.MeterSolidPropsLJ
meterPE - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
meterPE - Variable in class etomica.virial.ClusterSumExternalField
meterPE - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
meterPE1 - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
meterPE1 - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
meterPE1 - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
meterPE1 - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
meterPE2 - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
meterPE2 - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
meterPE2 - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
meterPE2 - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
MeterPhiDeviation - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterPhiDeviation(ISpace) - Constructor for class etomica.normalmode.MeterPhiDeviation
MeterPlaneSlip - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterPlaneSlip(ISpace, ISpecies, int, int, int) - Constructor for class etomica.normalmode.MeterPlaneSlip
MeterPositionCOM - Class in etomica.data.meter: Returns the instantaneous center-of-mass position, summed over all leaf atoms in a box, dividing by the number of atoms.
MeterPositionCOM(ISpace) - Constructor for class etomica.data.meter.MeterPositionCOM
meterPotential - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
meterPotential - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
meterPotential - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
meterPotential - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
meterPotential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
meterPotential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
meterPotential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
meterPotential - Variable in class etomica.normalmode.MeterBoltzmannHTTP
meterPotential - Variable in class etomica.normalmode.MeterDDP
meterPotential - Variable in class etomica.normalmode.MeterDP
meterPotential - Variable in class etomica.normalmode.MeterTargetTP
MeterPotentialEnergy - Class in etomica.data.meter: Meter for evaluation of the potential energy in a box.
MeterPotentialEnergy(IPotentialMaster) - Constructor for class etomica.data.meter.MeterPotentialEnergy
meterPotentialEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmann
meterPotentialEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmannDirect
meterPotentialEnergy - Variable in class etomica.models.nitrogen.MeterDirectInitPert
meterPotentialEnergy - Variable in class etomica.normalmode.MeterBoltzmann
MeterPotentialEnergyComposite(IPotentialMaster, IPotentialMaster, double, int) - Constructor for class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
MeterPotentialEnergyComposite(IPotentialMaster, IPotentialMaster, double, int) - Constructor for class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
MeterPotentialEnergyComposite(IPotentialMaster, IPotentialMaster, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
MeterPotentialEnergyComposite(IPotentialMaster, IPotentialMaster, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
MeterPotentialEnergyCutoff - Class in etomica.liquidLJ: Meter for evaluation of the potential energy in a box.
MeterPotentialEnergyCutoff(IPotentialMaster, ISpace, double[]) - Constructor for class etomica.liquidLJ.MeterPotentialEnergyCutoff
MeterPotentialEnergyDifference(DataSourceScalar, double) - Constructor for class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
MeterPotentialEnergyFromIntegrator - Class in etomica.data.meter: Acts as a DataSource to retrieve the energy from the integrator
MeterPotentialEnergyFromIntegrator() - Constructor for class etomica.data.meter.MeterPotentialEnergyFromIntegrator
MeterPotentialEnergyFromIntegrator(IntegratorBox) - Constructor for class etomica.data.meter.MeterPotentialEnergyFromIntegrator
meterPotentialMeasured - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
meterPotentialMeasured - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
meterPotentialSampled - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
meterPotentialSampled - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
MeterPressure - Class in etomica.data.meter: Meter for evaluation of the soft-potential pressure in a box.
MeterPressure(ISpace) - Constructor for class etomica.data.meter.MeterPressure
MeterPressure2 - Class in etomica.modules.vle: Meter for evaluation of the soft-potential pressure in a box.
MeterPressure2(ISpace) - Constructor for class etomica.modules.vle.MeterPressure2
MeterPressureByVolumeChange - Class in etomica.data.meter: Evaluates the pressure by examining the change in energy accompanying small changes in volume.
MeterPressureByVolumeChange(ISpace) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
MeterPressureByVolumeChange(ISpace, boolean[]) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
MeterPressureByVolumeChange(ISpace, BoxInflateDeformable) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
MeterPressureByVolumeChange(ISpace, boolean[], BoxInflateDeformable) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
MeterPressureByVolumeChange.DataSourceExp - Class in etomica.data.meter: Transforms the scaling from linear (-s to +s) to exponential (exp(-s) to exp(+s))
MeterPressureHard - Class in etomica.data.meter: Meter for the pressure (given as the compressibility factor) of a hard potential.
MeterPressureHard(ISpace) - Constructor for class etomica.data.meter.MeterPressureHard
MeterPressureHardTensor - Class in etomica.data.meter
MeterPressureHardTensor(ISpace) - Constructor for class etomica.data.meter.MeterPressureHardTensor
MeterPressureMolecular - Class in etomica.data.meter: Meter for evaluation of the soft-potential (molecular) pressure in a box.
MeterPressureMolecular(ISpace) - Constructor for class etomica.data.meter.MeterPressureMolecular
MeterPressureSuperBox - Class in etomica.normalmode: Meter for evaluation of the soft-potential pressure in a box.
MeterPressureSuperBox(ISpace) - Constructor for class etomica.normalmode.MeterPressureSuperBox
MeterPressureTensor - Class in etomica.data.meter: Meter for evaluation of the soft-potential pressure tensor in a box.
MeterPressureTensor(IPotentialMaster, ISpace) - Constructor for class etomica.data.meter.MeterPressureTensor
MeterPressureTensorFromIntegrator - Class in etomica.data.meter: Acts as a DataSource to retrieve the pressure from the integrator.
MeterPressureTensorFromIntegrator(ISpace) - Constructor for class etomica.data.meter.MeterPressureTensorFromIntegrator
MeterProfile - Class in etomica.data.meter: Meter that takes a (scalar) Meter and records its property as a 1-dimensional function of position in the simulation volume.
MeterProfile(ISpace, IRandom) - Constructor for class etomica.data.meter.MeterProfile: Default constructor sets profile along the x-axis, with 100 points in the profile.
MeterProfileByAtoms - Class in etomica.data.meter: Meter that takes a (scalar) Meter and records its property as a 1-dimensional function of position in the simulation volume.
MeterProfileByAtoms(ISpace) - Constructor for class etomica.data.meter.MeterProfileByAtoms: Default constructor sets profile along the y-axis, with 100 histogram points.
MeterProfileByVolume - Class in etomica.data.meter: Meter that takes a (scalar) Meter and records its property as a 1-dimensional function of position in the simulation volume.
MeterProfileByVolume(ISpace) - Constructor for class etomica.data.meter.MeterProfileByVolume: Default constructor sets profile along the y-axis, with 100 histogram points.
MeterProfileByVolumeAdsorption - Class in etomica.modules.adsorption
MeterProfileByVolumeAdsorption(ISpace) - Constructor for class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
MeterPU - Class in etomica.liquidLJ: Meter for evaluation of the soft-potential pressure in a box.
MeterPU(ISpace) - Constructor for class etomica.liquidLJ.MeterPU
MeterPUCut - Class in etomica.liquidLJ: Meter for evaluation of the soft-potential pressure in a box.
MeterPUCut(ISpace, double[]) - Constructor for class etomica.liquidLJ.MeterPUCut
MeterPUCutLS - Class in etomica.liquidLJ: Meter for evaluation of the soft-potential pressure in a box.
MeterPUCutLS(ISpace, int) - Constructor for class etomica.liquidLJ.MeterPUCutLS
MeterRadiusGyration - Class in etomica.data.meter: Meter for tabulation of the radius of gyration of a set of chain molecules.
MeterRadiusGyration(ISpace) - Constructor for class etomica.data.meter.MeterRadiusGyration
MeterRDF - Class in etomica.data.meter: Meter for tabulation of the atomic radial distribution function (RDF).
MeterRDF(ISpace) - Constructor for class etomica.data.meter.MeterRDF: Creates meter with default to compute pair correlation for all leaf atoms in a box.
MeterRDFCylinder - Class in etomica.modules.pistoncylinder: MeterRDF sublcass that properly calculates the RDF for the Piston/Cylinder apparatus.
MeterRDFCylinder(ISpace) - Constructor for class etomica.modules.pistoncylinder.MeterRDFCylinder
MeterRDFPC - Class in etomica.data.meter: Meter for tabulation of the atomic radial distribution function (RDF).
MeterRDFPC(ISpace, IPotentialMaster, IBox) - Constructor for class etomica.data.meter.MeterRDFPC: Creates meter with default to compute pair correlation for all leaf atoms in a box.
meterRef - Variable in class etomica.normalmode.MeterOverlapSwitch
meterRefEnergy - Variable in class etomica.normalmode.MeterBoltzmannTarget
MeterRotationDistributionGroup - Class in etomica.models.nitrogen: Meter that measures the spherical coordinate angles angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane) and x-axis angle[1]: is phi, angle between the molecular axis vector and z-axis
MeterRotationDistributionGroup(IBox, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterRotationDistributionGroup
MeterRotPerturbMolecule - Class in etomica.models.nitrogen: Meter that returns a Boltzmann factor difference between 2 systems: system 1 and 0 1: (Target System) sampled with an angle constraint, e.g.
MeterRotPerturbMolecule(IntegratorMC, IPotentialMaster, ISpecies, ISpace, ISimulation, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterRotPerturbMolecule
meters - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
meters - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
meters - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
meters - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
meters - Variable in class etomica.models.oneDHardRods.SimDifferentImage
meters - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
meters - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
meters - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
meters - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
meters - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
meters - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
meters - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
meters - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
meters - Variable in class etomica.normalmode.SimOverlap
meters - Variable in class etomica.normalmode.SimOverlapLJ
meters - Variable in class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
meters - Variable in class etomica.normalmode.SimOverlapLJModule
meters - Variable in class etomica.normalmode.SimOverlapModule
meters - Variable in class etomica.normalmode.SimOverlapSoftSphere
meters - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
meters - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
meters - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
meters - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
meters - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
meters - Variable in class etomica.normalmode.SimOverlapSSnxy
meters - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
meters - Variable in class etomica.virial.simulations.SimulationVirialOverlap
meters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
MeterSamplingHarmonic - Class in etomica.normalmode: Meter used for compute for the probability of the harmonic sampling < e0 / (e1 + alpha * e0)>umb
MeterSamplingHarmonic(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterSamplingHarmonic
MeterSamplingTarget - Class in etomica.normalmode: Meter used for compute for the probability of the target system sampling < e1 / (e1 + alpha * e0)>umb
MeterSamplingTarget(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterSamplingTarget
MeterSamplingWeight - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterSamplingWeight(DataSourceAtomDistance) - Constructor for class etomica.virial.MeterSamplingWeight: Constructor for MeterVirial.
MeterSolidDA - Class in etomica.normalmode: Meter for evaluation of the soft-potential pressure in a box.
MeterSolidDA(ISpace, IPotentialMaster, CoordinateDefinition, boolean) - Constructor for class etomica.normalmode.MeterSolidDA
MeterSolidDACut - Class in etomica.normalmode: Meter for evaluation of the soft-potential pressure in a box.
MeterSolidDACut(ISpace, IPotentialMaster, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.MeterSolidDACut
MeterSolidMirror - Class in etomica.normalmode: Meter uses harmonically-mapped averages to compute properties and also couples configurations with their mirror images to obtain cancellation of error at very low temperatures.
MeterSolidMirror(ISpace, IEtomicaDataSource, CoordinateDefinition) - Constructor for class etomica.normalmode.MeterSolidMirror
MeterSolidProps - Class in etomica.normalmode
MeterSolidProps(ISpace, DataSourceScalar, PotentialMaster, CoordinateDefinition, double, double, double, double, double, boolean) - Constructor for class etomica.normalmode.MeterSolidProps
MeterSolidPropsLJ - Class in etomica.normalmode
MeterSolidPropsLJ(ISpace, DataSourceScalar, PotentialMaster, CoordinateDefinition, double, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.normalmode.MeterSolidPropsLJ
MeterSpin - Class in etomica.spin: Meter that provides the x-component of the vector average of spin values (which is represented by the atom's position vector).
MeterSpin(ISpace) - Constructor for class etomica.spin.MeterSpin
MeterStrain - Class in etomica.modules.materialfracture
MeterStrain() - Constructor for class etomica.modules.materialfracture.MeterStrain
MeterStress - Class in etomica.modules.materialfracture: Meter that calculates the stress within the gage cell.
MeterStress(PotentialCalculationForceStress) - Constructor for class etomica.modules.materialfracture.MeterStress
MeterStructureFactor - Class in etomica.data.meter: Meter for calculation of structure factor of a group of atoms based on a particular wave vector.
MeterStructureFactor(ISpace, BravaisLatticeCrystal, IBox) - Constructor for class etomica.data.meter.MeterStructureFactor: Creates meter with default to compute the structure factor for all atoms in the box.
meterTarget - Variable in class etomica.normalmode.MeterOverlapSwitch
meterTarget - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
meterTarget - Variable in class etomica.normalmode.MeterWorkBennetTarget
meterTarget - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
meterTarget - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
MeterTargetRPMolecule - Class in etomica.models.nitrogen: Rotational Perturbation for beta-phase Nitrogen - scaling of the rotational angle to better map the phase space of the perturbing systems.
MeterTargetRPMolecule(IPotentialMaster, ISpecies, ISpace, ISimulation, CoordinateDefinitionNitrogen, PRotConstraint) - Constructor for class etomica.models.nitrogen.MeterTargetRPMolecule
MeterTargetTP - Class in etomica.normalmode: Meter that measures the overlap averages for perturbing from a solid at one temperature into other the system at other temperatures.
MeterTargetTP(IPotentialMaster, ISpecies, ISpace, ISimulation) - Constructor for class etomica.normalmode.MeterTargetTP
MeterTargetTPMolecule - Class in etomica.models.nitrogen: For molecular model, e.g., diatomic Nitrogen model, with 5 d.o.f.
MeterTargetTPMolecule(IPotentialMaster, ISpecies, ISpace, ISimulation) - Constructor for class etomica.models.nitrogen.MeterTargetTPMolecule
meterTemperature - Variable in class etomica.action.BoxQuench
MeterTemperature - Class in etomica.data.meter: Meter for measurement of the temperature based on kinetic-energy equipartition.
MeterTemperature(IBox, int) - Constructor for class etomica.data.meter.MeterTemperature
MeterTemperature(ISimulation, IBox, int) - Constructor for class etomica.data.meter.MeterTemperature
meterTemperature - Variable in class etomica.integrator.IntegratorGear4NPH
meterTemperature - Variable in class etomica.integrator.IntegratorMD
MeterTensorVelocity - Class in etomica.data.meter: A meter to compute the velocity component of the pressure tensor.
MeterTensorVelocity(ISpace) - Constructor for class etomica.data.meter.MeterTensorVelocity
MeterThetaDeviation - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterThetaDeviation(ISpace) - Constructor for class etomica.normalmode.MeterThetaDeviation
MeterTilt - Class in etomica.modules.sam: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTilt(ISpace, ISpecies) - Constructor for class etomica.modules.sam.MeterTilt
MeterTilt - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTilt(ISpace, ISpecies, int) - Constructor for class etomica.normalmode.MeterTilt
MeterTiltHistogram - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltHistogram(ISpace, ISpecies) - Constructor for class etomica.normalmode.MeterTiltHistogram
MeterTiltRotation - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltRotation(ISpace, ISpecies, int) - Constructor for class etomica.normalmode.MeterTiltRotation
MeterTiltRotationHistogram - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltRotationHistogram(ISpace, ISpecies, int) - Constructor for class etomica.normalmode.MeterTiltRotationHistogram
MeterTiltRotationStdev - Class in etomica.normalmode: Meter that measures the average tilt angle (not the angle of average tilt!)
MeterTiltRotationStdev(ISpace, ISpecies, int) - Constructor for class etomica.normalmode.MeterTiltRotationStdev
MeterUmbrella - Class in etomica.modules.multiharmonic.umbrella
MeterUmbrella(IEtomicaDataSource, IEtomicaDataSource, double) - Constructor for class etomica.modules.multiharmonic.umbrella.MeterUmbrella: Meter to measure the "overlap" function for free energy calculations, used as input to an AccumulatorVirialOverlapSingleAverage.
meterUmbrella - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
MeterVirial - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirial(ClusterAbstract[]) - Constructor for class etomica.virial.MeterVirial: Constructor for MeterVirial.
MeterVirialBD - Class in etomica.virial: This meter handles direct sampling with BigDecimal precision for averages.
MeterVirialBD(ClusterAbstract[]) - Constructor for class etomica.virial.MeterVirialBD: Constructor for MeterVirial.
MeterVirialBDBin - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialBDBin(ClusterWheatley, IRandom) - Constructor for class etomica.virial.MeterVirialBDBin: Constructor for MeterVirial.
MeterVirialBDBinMultiThreaded - Class in etomica.virial: Measures cluster averages for virial coefficients.
MeterVirialBDBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin) - Constructor for class etomica.virial.MeterVirialBDBinMultiThreaded: Constructor for MeterVirial.
MeterVirialBDBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, int, boolean) - Constructor for class etomica.virial.MeterVirialBDBinMultiThreaded
MeterVirialBDBinMultiThreaded.MyData - Class in etomica.virial
MeterVirialBinMultiThreaded - Class in etomica.virial: Measures cluster averages for virial coefficients.
MeterVirialBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin) - Constructor for class etomica.virial.MeterVirialBinMultiThreaded: Constructor for MeterVirial.
MeterVirialBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialBinMultiThreaded.MyData>, int, boolean) - Constructor for class etomica.virial.MeterVirialBinMultiThreaded
MeterVirialBinMultiThreaded.MyData - Class in etomica.virial
MeterVirialEBinMultiThreaded - Class in etomica.virial: Measures cluster averages for virial coefficients.
MeterVirialEBinMultiThreaded(ClusterWheatleyExtendSW, IRandom, IntSet.PropertyBin, int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded: Constructor for MeterVirial.
MeterVirialEBinMultiThreaded(ClusterWheatleyExtendSW, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, int, boolean, int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded
MeterVirialEBinMultiThreaded.MyData - Class in etomica.virial
MeterVirialEBinMultiThreaded.MyDataCov - Class in etomica.virial
MeterVirialExternalField - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalField(ClusterAbstract, double[]) - Constructor for class etomica.virial.MeterVirialExternalField: Constructor for MeterVirial.
MeterVirialExternalFieldConfined - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldConfined(ClusterAbstract, double[], double[]) - Constructor for class etomica.virial.MeterVirialExternalFieldConfined: Constructor for MeterVirial.
MeterVirialExternalFieldOverlapConfined - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapConfined(ExternalVirialDiagrams, MayerFunction, double[], double) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfined: Constructor for MeterVirial.
MeterVirialExternalFieldOverlapConfined.RangeComparator - Class in etomica.virial
MeterVirialExternalFieldOverlapConfinedRho - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapConfinedRho(ExternalVirialDiagrams, MayerFunction, double[], double, double, double, double) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho: Constructor for MeterVirial.
MeterVirialExternalFieldOverlapConfinedSW - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapConfinedSW(ExternalVirialDiagrams, MayerFunction, double[], double, double, double) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW: Constructor for MeterVirial.
MeterVirialExternalFieldOverlapRho - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldOverlapRho(ExternalVirialDiagrams, MayerFunction, double[]) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapRho: Constructor for MeterVirial.
MeterVirialExternalFieldRho - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldRho(ExternalVirialDiagrams, MayerFunction, double[]) - Constructor for class etomica.virial.MeterVirialExternalFieldRho: Constructor for MeterVirial.
MeterVirialExternalFieldSW - Class in etomica.virial: Measures value of clusters in a box and returns the values divided by the sampling bias from the sampling cluster.
MeterVirialExternalFieldSW(ClusterAbstract, double[], double, double, double) - Constructor for class etomica.virial.MeterVirialExternalFieldSW: Constructor for MeterVirial.
MeterVirialExternalFieldSW.Near - Class in etomica.virial
MeterVirialIC - Class in etomica.virial: Returns cluster and distribution function values from ClusterSumIC
MeterVirialIC(ClusterSumIC) - Constructor for class etomica.virial.MeterVirialIC: Constructor for MeterVirial.
MeterVirialSWWE - Class in etomica.virial
MeterVirialSWWE(ClusterWheatleyExtendSW) - Constructor for class etomica.virial.MeterVirialSWWE
MeterViscosity - Class in etomica.modules.rheology: Meter to measure the viscosity of a polymer in a shear field.
MeterViscosity(ISpace) - Constructor for class etomica.modules.rheology.MeterViscosity
MeterVolume - Class in etomica.data.meter: Meter for measurement of the box volume.
MeterVolume() - Constructor for class etomica.data.meter.MeterVolume
MeterWallForce - Class in etomica.interfacial
MeterWallForce(ISpace, IPotentialMaster, IBox, ISpecies) - Constructor for class etomica.interfacial.MeterWallForce
MeterWallForce.PotentialCalculationWallForce - Class in etomica.interfacial: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
MeterWallPosition - Class in etomica.interfacial
MeterWallPosition(IBox, ISpecies, double) - Constructor for class etomica.interfacial.MeterWallPosition
MeterWallPressure - Class in etomica.modules.sam
MeterWallPressure(PotentialCalculationForceSumWall) - Constructor for class etomica.modules.sam.MeterWallPressure
meterWidom - Variable in class etomica.modules.insertion.InsertionGraphic
MeterWidom() - Constructor for class etomica.modules.insertion.InsertionGraphic.MeterWidom
MeterWidomInsertion - Class in etomica.data.meter: Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a species via the Widom insertion method.
MeterWidomInsertion(ISpace, IRandom) - Constructor for class etomica.data.meter.MeterWidomInsertion
MeterWidomInsertionCorrection - Class in etomica.liquidLJ: Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a species via the Widom insertion method.
MeterWidomInsertionCorrection(ISpace, IRandom) - Constructor for class etomica.liquidLJ.MeterWidomInsertionCorrection
MeterWidomInsertionP - Class in etomica.liquidLJ: Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a species via the Widom insertion method.
MeterWidomInsertionP(ISpace, IRandom) - Constructor for class etomica.liquidLJ.MeterWidomInsertionP
MeterWidomMode - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterWidomMode(String, IPotentialMaster, CoordinateDefinition, IBox, int) - Constructor for class etomica.models.oneDHardRods.MeterWidomMode
MeterWidomModeImaginary - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterWidomModeImaginary(String, IPotentialMaster, CoordinateDefinition, IBox, int) - Constructor for class etomica.models.oneDHardRods.MeterWidomModeImaginary
MeterWidomModeReal - Class in etomica.models.oneDHardRods: Uses a Widom-like insertion of a mode to calculate a probability.
MeterWidomModeReal(String, IPotentialMaster, CoordinateDefinition, IBox, int) - Constructor for class etomica.models.oneDHardRods.MeterWidomModeReal
MeterWorkABandReweighting - Class in etomica.gaussianwork: Meter used for multiharmonic overlap sampling in the A-sampled system.
MeterWorkABandReweighting(IntegratorBox, PotentialMaster, double) - Constructor for class etomica.gaussianwork.MeterWorkABandReweighting
MeterWorkBAandReweighting - Class in etomica.gaussianwork: Meter used for overlap sampling in the B-sampled system.
MeterWorkBAandReweighting(IntegratorBox, PotentialMaster, double) - Constructor for class etomica.gaussianwork.MeterWorkBAandReweighting
MeterWorkBennetHarmonic - Class in etomica.normalmode: Meter used for direct sampling in the harmonic-sampled system.
MeterWorkBennetHarmonic(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkBennetHarmonic
MeterWorkBennetTarget - Class in etomica.normalmode: Meter used for direct sampling in the target-sampled system.
MeterWorkBennetTarget(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkBennetTarget
MeterWorkHarmonicBennet - Class in etomica.normalmode: Meter used for overlap sampling in the harmonic-sampled system.
MeterWorkHarmonicBennet(MCMoveHarmonic, PotentialMaster, double) - Constructor for class etomica.normalmode.MeterWorkHarmonicBennet
MeterWorkHarmonicPhaseSpace - Class in etomica.normalmode: Meter used for overlap sampling in the harmonic-sampled system.
MeterWorkHarmonicPhaseSpace(MCMoveHarmonic, PotentialMaster) - Constructor for class etomica.normalmode.MeterWorkHarmonicPhaseSpace
MeterWorkHarmonicTargetandReweighting - Class in etomica.normalmode: Meter used for overlap sampling in the harmonic-sampled system.
MeterWorkHarmonicTargetandReweighting(MCMoveHarmonic, PotentialMaster, double) - Constructor for class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
MeterWorkHarmonicUmbrella - Class in etomica.normalmode: Meter used for direct sampling in the harmonic-sampled system.
MeterWorkHarmonicUmbrella(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkHarmonicUmbrella
MeterWorkTargetBennet - Class in etomica.normalmode: Meter used for overlap sampling in the target-sampled system.
MeterWorkTargetBennet(IntegratorBox, MeterHarmonicEnergy, double) - Constructor for class etomica.normalmode.MeterWorkTargetBennet
MeterWorkTargetHarmonicandReweighting - Class in etomica.normalmode: Meter used for overlap sampling in the target-sampled system.
MeterWorkTargetHarmonicandReweighting(IntegratorBox, MeterHarmonicEnergy, double) - Constructor for class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
MeterWorkTargetPhaseSpace - Class in etomica.normalmode: Meter used for overlap sampling in the target-sampled system.
MeterWorkTargetPhaseSpace(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkTargetPhaseSpace
MeterWorkTargetUmbrella - Class in etomica.normalmode: Meter used for direct sampling in the target-sampled system.
MeterWorkTargetUmbrella(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkTargetUmbrella
MeterWorkUmbrellaHarmonic - Class in etomica.normalmode: Meter used for direct sampling in the harmonic-sampled system.
MeterWorkUmbrellaHarmonic(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterWorkUmbrellaHarmonic
MeterWorkUmbrellaTarget - Class in etomica.normalmode: Meter used for direct sampling in the target-sampled system.
MeterWorkUmbrellaTarget(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterWorkUmbrellaTarget
MethanolPotentialHelper - Class in etomica.models.rowley
MethanolPotentialHelper() - Constructor for class etomica.models.rowley.MethanolPotentialHelper
MethanolPotentialHelper - Class in etomica.models.traPPE
MethanolPotentialHelper() - Constructor for class etomica.models.traPPE.MethanolPotentialHelper
MethanolRouteParams - Class in etomica.models.rowley
MethanolRouteParams() - Constructor for class etomica.models.rowley.MethanolRouteParams
MethodNotImplementedException - Exception in etomica.exception: Exception that indicates a method is defined for a class (perhaps to adhere to an interface), but its implementation is not yet completed.
MethodNotImplementedException() - Constructor for exception etomica.exception.MethodNotImplementedException: Constructor for MethodNotImplementedException.
MethodNotImplementedException(String) - Constructor for exception etomica.exception.MethodNotImplementedException: Constructor for MethodNotImplementedException.
MethodNotImplementedException(String, Throwable) - Constructor for exception etomica.exception.MethodNotImplementedException: Constructor for MethodNotImplementedException.
MethodNotImplementedException(Throwable) - Constructor for exception etomica.exception.MethodNotImplementedException: Constructor for MethodNotImplementedException.
metricPanel - Variable in class etomica.graphics.SimulationPanel
MEv1v2(IVector, IVector) - Method in interface etomica.space.Tensor
MEv1v2(IVector, IVector) - Method in class etomica.space1d.Tensor1D
MEv1v2(IVector, IVector) - Method in class etomica.space2d.Tensor2D
MEv1v2(IVector, IVector) - Method in class etomica.space3d.Tensor3D
MEv1v2(IVector, IVector) - Method in class etomica.spaceNd.TensorND
mFe - Variable in class etomica.meam.PotentialFeEAM_LS
mfp - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
mfp - Variable in class etomica.graph.operations.Decorate.DecorateParameters
mfp - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
mfp - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
mfp - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
mfp - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
mfp - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
mH - Static variable in class etomica.potential.P2WaterPotentialsJankowski
mH2O - Static variable in class etomica.potential.P2WaterPotentialsJankowski
MICRO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-6.
millerPlane - Variable in class etomica.dimer.SimDimerMEAMGB
millerRabin(BigInteger) - Method in class etomica.veos.bigdecimal.Prime: Miller-Rabin primality tests.
MILLI - Static variable in class etomica.units.Prefix: Prefix indicating 10^-3 = 0.001.
mimeTypeMap - Static variable in class etomica.graph.view.rasterizer.Main: Static map containing all the mime types understood by the rasterizer
min(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Minimum of two values.
min(Vector<Ifactor>) - Static method in class etomica.veos.bigdecimal.Ifactor: Minimum of a list of values.
min(Rational) - Method in class etomica.veos.bigdecimal.Rational: Compares the value of this with another constant.
min - Static variable in class org.jmol.script.Token
MIN_INT - Static variable in class etomica.veos.bigdecimal.Rational
MIN_X - Static variable in class etomica.graphics.DevicePlotPoints
MIN_Y - Static variable in class etomica.graphics.DevicePlotPoints
minbonddistance - Static variable in class org.jmol.script.Token
mincf - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
minDiffLocation() - Method in class etomica.virial.overlap.DataSourceVirialOverlap: Returns the index of the Bennet parameter which minimizes the differences between the Bennet "sums" from the target and references accumulators.
minDiffLocation() - Method in class etomica.virial.overlap.DataVirialOverlap: Deprecated.
minDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
minFlipDistance - Variable in class etomica.virial.ClusterCoupledFlipped
minFloat - Variable in class etomica.graphics.DisplayTable
minFound - Variable in class etomica.dimer.IntegratorDimerMin
MINIMIZATION_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
MinimizationBetaNitrogenModel - Class in etomica.models.nitrogen: Lattice-Energy Minimization for Beta-Nitrogen Structure using gradient
MinimizationBetaNitrogenModel(ISpace, int[], double) - Constructor for class etomica.models.nitrogen.MinimizationBetaNitrogenModel
MinimizationBetaNitrogenModelLS - Class in etomica.models.nitrogen: Lattice-Energy Minimization for Beta-Nitrogen Structure using gradient with lattice sum
MinimizationBetaNitrogenModelLS(ISpace, double, double) - Constructor for class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
minimizationcriterion - Static variable in class org.jmol.script.Token
minimizationrefresh - Static variable in class org.jmol.script.Token
minimizationsilent - Static variable in class org.jmol.script.Token
minimizationsteps - Static variable in class org.jmol.script.Token
MinimizationTIP4P - Class in etomica.models.clathrates
MinimizationTIP4P(ISpace, double, double, double[], int[], int, boolean, double, String, boolean) - Constructor for class etomica.models.clathrates.MinimizationTIP4P
MinimizationTIP4P.ChargeAgentSourceRPM - Class in etomica.models.clathrates
MinimizationTIP4P.SimParams - Class in etomica.models.clathrates
minimize(double[], double, int) - Method in class etomica.util.numerical.NewtonMinimization
minimize(double[], double[], double, int) - Method in class etomica.util.numerical.SteepestDescent
MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JmolConstants
MinimizeBetaNitrogenLatticeParameter - Class in etomica.models.nitrogen: This class is written to minimize the lattice energy of the beta-phase Nitrogen, which has HCP packing with 2 basis atoms using line minimization The varying parameters are: unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9]) unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9]) - 3 translational + 2 rotational There are total of 20 degrees of freedom.
MinimizeBetaNitrogenLatticeParameter(ISpace, int[], double) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
MinimizeBetaNitrogenLatticeParameterFromFile - Class in etomica.models.nitrogen: This class is written to minimize the lattice energy of the beta-phase Nitrogen, which has HCP packing with 2 basis atoms using line minimization The varying parameters are: unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9]) unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9]) - 3 translational + 2 rotational There are total of 20 degrees of freedom.
MinimizeBetaNitrogenLatticeParameterFromFile(ISpace, int[], double, double[]) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
MinimizeBetaNitrogenLatticeParameterLSFromFile - Class in etomica.models.nitrogen: This class is written to minimize the lattice energy of the beta-phase Nitrogen, which has HCP packing with 2 basis atoms using line minimization The varying parameters are: unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9]) unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9]) - 3 translational + 2 rotational There are total of 20 degrees of freedom.
MinimizeBetaNitrogenLatticeParameterLSFromFile(ISpace, double, double[], double) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
MinimizeBetaNitrogenTranslationDOF - Class in etomica.models.nitrogen: This class is written to minimize the lattice energy of the beta-phase Nitrogen, which has HCP packing with 2 basis atoms using line minimization The varying parameters are all the translational d.o.f of the molecules NO rotational d.o.f.
MinimizeBetaNitrogenTranslationDOF(ISpace, int[], double, String, double) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
MinimizeGammaNitrogenLatticeParameter - Class in etomica.models.nitrogen: Determine c/a ratio for tetragonal unit cell that minimizes the lattice energy of gamma-N2 crystal structure gamma-N2 crystal Structure
MinimizeGammaNitrogenLatticeParameter(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
MinimizeHCP - Class in etomica.normalmode: Determines c/a ratio of primitive vector lengths corresponding to the minimum energy HCP structure.
MinimizeHCP(Space, int, double, int, double, double) - Constructor for class etomica.normalmode.MinimizeHCP
MinimizeHCP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
minimum(P2QChemInterpolated) - Method in class etomica.potential.P2QChemInterpolated
minimum() - Method in class etomica.util.DoubleRange: The minimium defined by this range.
minimum() - Method in class etomica.util.IntegerRange: The minimium defined by this range.
minimumScreening(double, double) - Method in class etomica.util.numerical.B9Optimizer
minimumScreening(int, int, double, double) - Method in class etomica.util.numerical.VirialOptimizer
minMu - Variable in class etomica.normalmode.DataSourceMuRoot1
minMulti - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
minMulti - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
minMultiP - Variable in class etomica.virial.cluster.VirialDiagrams
minMultiP - Variable in class etomica.virial.cluster.VirialDiagramsPT
minN - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
minNumAtoms - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
minOCOr2 - Variable in class etomica.modules.catalysis.P2SquareWellBonding
minOOr2 - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
minor(BigInteger[][], int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Minor of an integer matrix.
minpixelselradius - Static variable in class org.jmol.script.Token
minR - Variable in class etomica.models.co2.P2CO2H2OWheatley
minR2 - Variable in class etomica.association.AssociationHelperBranched
minR2 - Variable in class etomica.association.AssociationHelperDouble
minR2 - Variable in class etomica.association.AssociationHelperMolecule
minRadicalSites - Variable in class etomica.modules.catalysis.P2SquareWellSurface
minSearch - Variable in class etomica.dimer.SimDimerLJadatom
minus(Complex) - Method in class etomica.math.Complex: Subtraction of Complex numbers (doesn't change this Complex number).
minus(Matrix) - Method in class etomica.math.linearalgebra.Matrix
minus_half_sqrt_bondlength - Static variable in class etomica.virial.ConformationPh3site
mip - Variable in class etomica.graph.property.FFTDecomposition
mip - Variable in class etomica.graph.property.IsFFT
MIXED - Static variable in class etomica.units.Dimension: Dimension used to indicate that a group of values are not all of the same dimension.
mixF - Variable in class etomica.virial.ClusterWheatleySoftBDMix
mixF - Variable in class etomica.virial.ClusterWheatleySoftMix
mixFMulti3 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
mixID - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
mixPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
mixPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
mixPotentialsM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
mixPotentialsP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
MKS - Class in etomica.units.systems: Meter-Kilogram-Second system of units
MKS() - Constructor for class etomica.units.systems.MKS
mLREP - Variable in class etomica.meam.PotentialCuLREP
mmBond - Variable in class etomica.virial.cluster.VirialDiagrams
mmBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
mNumBody - Variable in class etomica.virial.cluster.ClusterDiagram
mNumIdenticalPermutations - Variable in class etomica.virial.cluster.ClusterDiagram
mO - Static variable in class etomica.potential.P2WaterPotentialsJankowski
mo - Static variable in class org.jmol.script.Token
mobileSpecies - Variable in class etomica.config.GrainBoundaryTiltConfiguration
mod(IVector) - Method in interface etomica.api.IVectorMutable: Replaces each component of this vector with its value modulo the corresponding component in u
mod(IVector) - Method in class etomica.space1d.Vector1D
mod(Vector1D) - Method in class etomica.space1d.Vector1D
mod(IVector) - Method in class etomica.space2d.Vector2D
mod(IVector) - Method in class etomica.space3d.Vector3D
mod(Vector3D) - Method in class etomica.space3d.Vector3D
mod(IVector) - Method in class etomica.spaceNd.VectorND
mod2pi(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Reduce value to the interval [0,2*Pi].
Model - Class in etomica.chem.models: Top-level class for a molecular model.
Model(boolean) - Constructor for class etomica.chem.models.Model
model - Static variable in class org.jmol.script.Token
Model.PotentialAndIterator - Class in etomica.chem.models: Wrapper class for a Potential and an AtomsetIteratorBasisDependent that is associated with the potential.
ModelAlertMsgDialog - Class in etomica.virial.GUI.models
ModelAlertMsgDialog(String) - Constructor for class etomica.virial.GUI.models.ModelAlertMsgDialog
ModelAlkaneLengthSelection - Class in etomica.virial.GUI.models
ModelAlkaneLengthSelection() - Constructor for class etomica.virial.GUI.models.ModelAlkaneLengthSelection
ModelChain - Class in etomica.chem.models: Model class for a simple chain molecule (homopolymer)
ModelChain(ISpace, boolean) - Constructor for class etomica.chem.models.ModelChain: Constructs a default ModelChain instance.
modelindex - Static variable in class org.jmol.script.Token
modelIndex - Variable in class org.jmol.util.Point3fi
MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JmolConstants
MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JmolConstants
modelkitmode - Static variable in class org.jmol.script.Token
ModelMoleculeListDisplayTable - Class in etomica.virial.GUI.models
ModelMoleculeListDisplayTable() - Constructor for class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
ModelMoleculeListDisplayTable_new - Class in etomica.virial.GUI.models
ModelMoleculeListDisplayTable_new() - Constructor for class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
ModelPotParamDisplayTable - Class in etomica.virial.GUI.models
ModelPotParamDisplayTable() - Constructor for class etomica.virial.GUI.models.ModelPotParamDisplayTable
modelSelectedSpecies - Variable in class etomica.virial.GUI.models.AppModelMixtureBuilder
ModelSelectedSpecies - Class in etomica.virial.GUI.models
ModelSelectedSpecies() - Constructor for class etomica.virial.GUI.models.ModelSelectedSpecies
ModelSimulationConstructor - Class in etomica.virial.GUI.models
ModelSimulationConstructor() - Constructor for class etomica.virial.GUI.models.ModelSimulationConstructor
ModelSimulationEnvironment - Class in etomica.virial.GUI.models
ModelSimulationEnvironment() - Constructor for class etomica.virial.GUI.models.ModelSimulationEnvironment
ModelSimulationEnvironment(double, int, ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.models.ModelSimulationEnvironment
ModelSimulationEnvironment(double, int) - Constructor for class etomica.virial.GUI.models.ModelSimulationEnvironment
modelSpeciesSelection - Variable in class etomica.virial.GUI.models.AppModelMixtureBuilder
ModelSpeciesSelection - Class in etomica.virial.GUI.models
ModelSpeciesSelection() - Constructor for class etomica.virial.GUI.models.ModelSpeciesSelection
ModelTemperatureAndSteps - Class in etomica.virial.GUI.models
modeNum - Variable in class etomica.normalmode.MCMoveHarmonic
modes - Variable in class etomica.normalmode.MCMoveHarmonicStep
modeSigns - Variable in class etomica.dimer.SimDimerLJadatom
modeSigns - Variable in class etomica.dimer.SimDimerMEAMadatom
modeSigns - Variable in class etomica.dimer.SimDimerMEAMGB
modeSigns - Variable in class etomica.kmc.SimKMCMEAMadatom
Modifier - Interface in etomica.modifier: A Modifier object permits changes to be made to a property of another object.
ModifierAtomDiameter(MuGraphic, SpeciesSpheresMono, P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide) - Constructor for class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
ModifierAtomDiameter() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
ModifierAtomDiameter(SpeciesSpheresMono, P2LennardJones, SpeciesSpheresMono[], P2LennardJones[], DiameterHashByType) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
ModifierAtomDiameter(SpeciesSpheresMono, P2LennardJones, P2LennardJones[], P2LennardJones[], DiameterHashByType) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
ModifierAtomDiameter() - Constructor for class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
ModifierBoolean - Interface in etomica.modifier: Interface that permits changes to be made to a boolean property of another object.
ModifierBoxSize(ISpace, IBox, int, IAction) - Constructor for class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
ModifierBoxSize(ISpace, IBox, int, IAction) - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
ModifierCells3D - Class in etomica.normalmode: Modifier class that enables change of the number of cells in 2D
ModifierCells3D(IBox, ISpecies) - Constructor for class etomica.normalmode.ModifierCells3D
ModifierDimensions - Class in etomica.modules.entropylottery
ModifierDimensions(ISpace, IBox) - Constructor for class etomica.modules.entropylottery.ModifierDimensions
ModifierEpsilon(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.ModifierEpsilon
ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
ModifierFunctionWrapper - Class in etomica.modifier: Extends the configurable modifier to permit a function to be applied to a value before the modified property is set.
ModifierFunctionWrapper(Object[], String) - Constructor for class etomica.modifier.ModifierFunctionWrapper
ModifierFunctionWrapper(Object, String) - Constructor for class etomica.modifier.ModifierFunctionWrapper
ModifierGeneral - Class in etomica.modifier: Implements the Modifier functionality using introspection to obtain the accessor methods for a property.
ModifierGeneral(Object[], String) - Constructor for class etomica.modifier.ModifierGeneral: Constructor connecting the modifier's getValue and setValue methods to the set/get accessor methods of the object being modifier.
ModifierGeneral(Object, String) - Constructor for class etomica.modifier.ModifierGeneral: Modifier for property of a single object (most common use)
ModifierLambda(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.ModifierLambda
ModifierNMolecule - Class in etomica.modifier: Modifier class that enables change of the number of molecules of a particular species in a particular box.
ModifierNMolecule(IBox, ISpecies) - Constructor for class etomica.modifier.ModifierNMolecule
ModifierPistonDensity() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
ModifierPistonPressure - Class in etomica.modules.pistoncylinder: Modifier for the piston pressure.
ModifierPistonPressure(ISpace, P1HardMovingBoundary, Dimension) - Constructor for class etomica.modules.pistoncylinder.ModifierPistonPressure
ModifierPMu - Class in etomica.modules.adsorption
ModifierPMu(P2SquareWell, IntegratorBox, EOSSW, MyMCMove, MeterExcessAdsorbed) - Constructor for class etomica.modules.adsorption.ModifierPMu
ModifierSoluteCharge(P2Electrostatic, P2Electrostatic, P2Electrostatic, P2Electrostatic[], P2Electrostatic[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
ModifierTPI - Class in etomica.virial.simulations
ModifierTPI(double, int, MCMoveClusterRingRegrow, MCMoveClusterRingRegrow, ClusterAbstract) - Constructor for class etomica.virial.simulations.ModifierTPI
ModifierWallPosition(Sam) - Constructor for class etomica.modules.sam.SamGraphic.ModifierWallPosition
ModifierXCells2D - Class in etomica.normalmode: Modifier class that enables change of the number of cells in 2D
ModifierXCells2D(IBox, ISpecies, int) - Constructor for class etomica.normalmode.ModifierXCells2D
ModifierYCells2D - Class in etomica.normalmode: Modifier class that enables change of the number of cells in 2D
ModifierYCells2D(IBox, ISpecies, int) - Constructor for class etomica.normalmode.ModifierYCells2D
modify - Static variable in class org.jmol.script.Token
modifyAction - Variable in class etomica.graphics.DeviceBox: Modifier connecting the slider to the property
modifyAction - Variable in class etomica.graphics.DeviceSlider: Modifier connecting the slider to the property
modifyAction - Variable in class etomica.graphics.DeviceSpinner: Modifier connecting the spinner to the property
ModifyAction - Class in etomica.modifier: Wraps a Modifier instance so that the modification can be performed as the consequence of an action.
ModifyAction(Modifier) - Constructor for class etomica.modifier.ModifyAction: Constuctor requires the wrapped Modifier, which is final.
modifyorcreate - Static variable in class org.jmol.script.Token
modpi(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Reduce value to the interval [-Pi/2,Pi/2].
modulus() - Method in class etomica.math.Complex: Modulus of this Complex number, the distance from the origin in polar coordinates.
moebius() - Method in class etomica.veos.bigdecimal.Ifactor: The Moebius function.
molAVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
molAVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
molAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
molBVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
molBVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
Mole - Class in etomica.units: The mole unit of quantity, approximately equal to 6.022e23 simulation units.
molecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
molecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
MolecularModel2CLJQ_SpeciesCO2 - Class in etomica.virial.GUI.models
MolecularModel2CLJQ_SpeciesCO2() - Constructor for class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
MolecularModel2CLJQ_SpeciesEthane - Class in etomica.virial.GUI.models
MolecularModel2CLJQ_SpeciesEthane() - Constructor for class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
MolecularModel2CLJQ_SpeciesLJ - Class in etomica.virial.GUI.models
MolecularModel2CLJQ_SpeciesLJ() - Constructor for class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
MolecularModelEMP2_SpeciesCO2 - Class in etomica.virial.GUI.models
MolecularModelEMP2_SpeciesCO2() - Constructor for class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
MolecularModelExp6_SpeciesAlkane - Class in etomica.virial.GUI.models
MolecularModelExp6_SpeciesAlkane() - Constructor for class etomica.virial.GUI.models.MolecularModelExp6_SpeciesAlkane
MolecularModelLJ_SpeciesLJ - Class in etomica.virial.GUI.models
MolecularModelLJ_SpeciesLJ() - Constructor for class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
MolecularModelLJQ_SpeciesLJ - Class in etomica.virial.GUI.models
MolecularModelLJQ_SpeciesLJ() - Constructor for class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
MolecularModelSKS_SpeciesAlkane - Class in etomica.virial.GUI.models
MolecularModelSKS_SpeciesAlkane() - Constructor for class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
MolecularModelSKS_SpeciesAlkane(int) - Constructor for class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
MolecularModelSPCE_SpeciesH2O - Class in etomica.virial.GUI.models
MolecularModelSPCE_SpeciesH2O() - Constructor for class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
MolecularModelTRAPPE_SpeciesAlkane - Class in etomica.virial.GUI.models
MolecularModelTRAPPE_SpeciesAlkane() - Constructor for class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
MolecularModelTRAPPE_SpeciesAlkane(int) - Constructor for class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
MolecularModelTrappe_SpeciesCO2 - Class in etomica.virial.GUI.models
MolecularModelTrappe_SpeciesCO2() - Constructor for class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
molecularPotentials - Variable in class etomica.potential.PotentialMasterLrc
MolecularWeightAvg - Class in etomica.modules.chainequilibrium: Takes output from MeterChainLength as input and outputs the number-average molecular weight.
MolecularWeightAvg() - Constructor for class etomica.modules.chainequilibrium.MolecularWeightAvg
MolecularWeightAvg2 - Class in etomica.modules.chainequilibrium: Takes output from MeterChainLength as input and outputs the weight-average molecular weight.
MolecularWeightAvg2() - Constructor for class etomica.modules.chainequilibrium.MolecularWeightAvg2
Molecule - Class in etomica.atom
Molecule(ISpecies, int) - Constructor for class etomica.atom.Molecule
molecule - Variable in class etomica.box.BoxMoleculeEvent
molecule - Variable in class etomica.integrator.mcmove.MCMoveMolecule
molecule - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
molecule - Static variable in class org.jmol.script.Token
molecule0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
molecule0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
molecule0 - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
molecule0 - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
molecule1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
molecule1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
molecule1 - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
molecule1 - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
MOLECULE1_INDEX - Static variable in class etomica.util.Debug: Molecule index of a molecule of interest.
MOLECULE2_INDEX - Static variable in class etomica.util.Debug: Global index of a molecule of interest.
MoleculeAction - Interface in etomica.action: Interface for a class that can perform an action on an atom.
MoleculeActionRelaxWater3P - Class in etomica.virial
MoleculeActionRelaxWater3P(ISpace) - Constructor for class etomica.virial.MoleculeActionRelaxWater3P
MoleculeActionTranslateTo - Class in etomica.action: Moves (translates) an atom to a specified position.
MoleculeActionTranslateTo(ISpace) - Constructor for class etomica.action.MoleculeActionTranslateTo: Creates new action with atom position defined by its center of mass (via AtomPositionCOM).
moleculeAdded(IMolecule) - Method in class etomica.box.BoxEventManager
MoleculeAgent(ISpace) - Constructor for class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
MoleculeAgent(ISpace) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
MoleculeAgent(ISpace) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
moleculeAgentIterator - Variable in class etomica.potential.PotentialCalculationTorqueSum
moleculeAgentManager - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
MoleculeAgentManager - Class in etomica.atom: MoleculeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every IMolecule in a box.
MoleculeAgentManager(ISimulation, IBox, MoleculeAgentManager.MoleculeAgentSource) - Constructor for class etomica.atom.MoleculeAgentManager
moleculeAgentManager - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
moleculeAgentManager - Variable in class etomica.integrator.IntegratorRigidIterative
moleculeAgentManager - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
moleculeAgentManager - Variable in class etomica.potential.PotentialCalculationTorqueSum
moleculeAgentManager - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
MoleculeAgentManager.AgentIterator - Class in etomica.atom: Iterator that loops over the agents, skipping null elements
MoleculeAgentManager.MoleculeAgentSource - Interface in etomica.atom: Interface for an object that wants an agent associated with each IMolecule an IBox.
MoleculeArrayList - Class in etomica.atom
MoleculeArrayList() - Constructor for class etomica.atom.MoleculeArrayList
MoleculeArrayList(int) - Constructor for class etomica.atom.MoleculeArrayList
moleculeCell0 - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
moleculeCenter - Variable in class etomica.action.BoxInflate
moleculeCenter - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
moleculeCenter - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
MoleculeChildAtomAction - Class in etomica.action: Wraps an AtomAction, and performs the wrapped action on the atom only if it is a leaf atom; if given an atom group (as indicated by the atom's node), performs action instead on all the atom's child atoms.
MoleculeChildAtomAction(AtomAction) - Constructor for class etomica.action.MoleculeChildAtomAction: Constructor takes wrapped action, which is final.
moleculeForce - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
moleculeIndexChanged(IMolecule, int) - Method in class etomica.box.BoxEventManager
moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibody
moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
MoleculeInfoBrute(ISpace) - Constructor for class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
moleculeIterator - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
MoleculeIterator - Interface in etomica.atom.iterator: Interface for classes that loop over a set of atoms.
MoleculeIterator0() - Constructor for class etomica.potential.PotentialMaster.MoleculeIterator0
MoleculeIteratorAll - Class in etomica.atom.iterator: Iterator for all the molecules of a set of species in a box.
MoleculeIteratorAll(ISpecies[]) - Constructor for class etomica.atom.iterator.MoleculeIteratorAll
MoleculeIteratorAll(ISpecies[], boolean) - Constructor for class etomica.atom.iterator.MoleculeIteratorAll
MoleculeIteratorAllMolecules - Class in etomica.atom.iterator: Iterator for all the molecules in a box.
MoleculeIteratorAllMolecules() - Constructor for class etomica.atom.iterator.MoleculeIteratorAllMolecules
MoleculeIteratorAllMolecules(IBox) - Constructor for class etomica.atom.iterator.MoleculeIteratorAllMolecules: Returns a new iterator ready to iterate over the molecules of the given box.
MoleculeIteratorArrayList - Class in etomica.atom.iterator: An atom iterator of the elements from an AtomArrayList (in proper sequence).
MoleculeIteratorArrayList(IteratorDirective.Direction, int, MoleculeToIndex, MoleculeToMoleculeList) - Constructor for class etomica.atom.iterator.MoleculeIteratorArrayList
MoleculeIteratorArrayListSimple - Class in etomica.atom.iterator: An atom iterator of the elements from an AtomArrayList (in proper sequence).
MoleculeIteratorArrayListSimple() - Constructor for class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Constructs new iterator with an empty list.
MoleculeIteratorArrayListSimple(IMoleculeList) - Constructor for class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Constructs new iterator set to iterate given list (upon reset).
MoleculeIteratorBoxDependent - Interface in etomica.atom.iterator: Interface indicating that an atom iterator can determine appropriate atoms for iteration given an arbitrary box.
MoleculeIteratorCell - Class in etomica.nbr.cell.molecule: Returns occupants of all cells as iterates.
MoleculeIteratorCell(int, BoxAgentManager) - Constructor for class etomica.nbr.cell.molecule.MoleculeIteratorCell: Constructor makes iterator that must have box specified and then be reset() before iteration.
MoleculeIteratorMolecule - Class in etomica.atom.iterator: Iterator for the molecules of a single species in a box.
MoleculeIteratorMolecule(ISpecies) - Constructor for class etomica.atom.iterator.MoleculeIteratorMolecule
MoleculeIteratorMoleculeDependent - Interface in etomica.atom.iterator: Interface for an atom iterator that can be altered by setting of an atom.
MoleculeIteratorSinglet - Class in etomica.atom.iterator: Iterator that expires after returning a single atom, which is specified by a call to the setAtom method, or via the constructor.
MoleculeIteratorSinglet() - Constructor for class etomica.atom.iterator.MoleculeIteratorSinglet: Constructs iterator without defining atom.
MoleculeIteratorSinglet(IMolecule) - Constructor for class etomica.atom.iterator.MoleculeIteratorSinglet: Constructs iterator specifying that it return the given atom.
moleculeList - Variable in class etomica.action.IntegratorDimerApproach
moleculeList - Variable in class etomica.atom.MoleculeToMoleculeListSpecies
moleculeList - Variable in class etomica.data.meter.MeterStructureFactor
moleculeList - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
moleculeList - Variable in class etomica.potential.EwaldSummation
moleculeList - Variable in class etomica.potential.EwaldSumMolecules
moleculeList - Variable in class etomica.virial.ClusterSumMultibody
moleculeList - Variable in class etomica.virial.PotentialNonAdditive
moleculeLists - Variable in class etomica.box.AtomSetAllMolecules
moleculeLists - Variable in class etomica.box.Box
MoleculeListWrapper - Class in etomica.atom: AtomSet formed by wrapping an AtomArrayList.
MoleculeListWrapper() - Constructor for class etomica.atom.MoleculeListWrapper: Wraps a new atom array of the given length.
MoleculeListWrapper(IMoleculeList) - Constructor for class etomica.atom.MoleculeListWrapper: Makes a new instance holding the atoms in the given atom set.
MoleculeListWrapper(MoleculeArrayList) - Constructor for class etomica.atom.MoleculeListWrapper: Wraps the given atom array.
MoleculeNeighborLists - Class in etomica.nbr.list.molecule: Class used to maintain neighbor lists.
MoleculeNeighborLists() - Constructor for class etomica.nbr.list.molecule.MoleculeNeighborLists: Constructs sequencer for the given molecule.
moleculeOffset - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
moleculeOffset - Variable in class etomica.modules.sam.ConfigurationSAM
MoleculeOriented - Class in etomica.atom: Molecule class appropriate for a rigid molecule.
MoleculeOriented(ISpace, ISpecies, int) - Constructor for class etomica.atom.MoleculeOriented
MoleculeOriented(ISpace, ISpecies, int, boolean) - Constructor for class etomica.atom.MoleculeOriented
MoleculeOrientedDynamic - Class in etomica.atom: Molecule class appropriate for a rigid molecule in a dynamic context.
MoleculeOrientedDynamic(ISpace, ISpecies, int) - Constructor for class etomica.atom.MoleculeOrientedDynamic
moleculePair - Variable in class etomica.atom.iterator.ANIntergroupExchange
MoleculePair - Class in etomica.atom: Data structure that contains two mutable atom instances.
MoleculePair() - Constructor for class etomica.atom.MoleculePair
MoleculePair(IMolecule, IMolecule) - Constructor for class etomica.atom.MoleculePair
moleculePair - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
MoleculePotential1ListSource(PotentialMasterListMolecular) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
MoleculePotentialList - Class in etomica.nbr.list.molecule: Class used to maintain list of whether each 1-body potential that applies to a species is currently in effect or not for an Molecule.
MoleculePotentialList() - Constructor for class etomica.nbr.list.molecule.MoleculePotentialList: Constructs sequencer for the given atom.
moleculeRemoved(IMolecule) - Method in class etomica.box.BoxEventManager
molecules - Variable in class etomica.atom.MoleculeArrayList
molecules - Variable in class etomica.normalmode.CoordinateDefinition.BasisCell
molecules - Variable in class etomica.virial.ClusterWheatleyMultibody
molecules - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
molecules - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
MoleculesetArray - Class in etomica.atom: AtomSet formed by wrapping an Atom array.
MoleculesetArray(int) - Constructor for class etomica.atom.MoleculesetArray: Wraps a new atom array of the given length.
MoleculesetArray(IMoleculeList) - Constructor for class etomica.atom.MoleculesetArray: Makes a new instance holding the atoms in the given atom set.
MoleculesetArray(MoleculesetArray) - Constructor for class etomica.atom.MoleculesetArray: Copy constructor, wrapping a new array unique to this instance but holding the same atoms as the given atom set.
MoleculesetArray(IMolecule[]) - Constructor for class etomica.atom.MoleculesetArray: Wraps the given atom array.
MoleculesetIterator - Interface in etomica.atom.iterator: Interface for classes that loop over a set of atoms.
MoleculesetIteratorBasisDependent - Interface in etomica.atom.iterator: Interface for an MoleculeIterator that can be conditioned with target and basis molecules.
MoleculesetIteratorBoxDependent - Interface in etomica.atom.iterator: Interface indicating that an iterator can determine appropriate atoms for iteration given an arbitrary box.
MoleculesetIteratorCellular - Interface in etomica.nbr.cell.molecule: Interface for moleculeset iterators that use cell-based neighbor lists for iteration.
MoleculesetIteratorPDT - Interface in etomica.atom.iterator: This is an interface for iterators that are box dependent, directable, and targetable.
MoleculesetIteratorTargetable - Interface in etomica.atom.iterator: Interface for an iterator that can be targeted at one or more atoms.
MoleculeSetSinglet - Class in etomica.atom: Data structure that contains a single mutable atom instance.
MoleculeSetSinglet() - Constructor for class etomica.atom.MoleculeSetSinglet
MoleculeSetSinglet(IMolecule) - Constructor for class etomica.atom.MoleculeSetSinglet
moleculeSetSinglet - Variable in class etomica.nbr.cell.molecule.MoleculeIteratorCell
moleculeSetSinglet - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
moleculeSetSinglet - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
moleculeSite - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
moleculeSite - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
moleculeSiteManager - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
moleculeSiteManager - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
MoleculeSiteSource(ISpace, IAtomPositionDefinition) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
MoleculeSiteSource(ISpace, IAtomPositionDefinition) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
MoleculeSource - Interface in etomica.atom: Interface for objects when return atoms (meeting some specification) from a box.
moleculeSource - Variable in class etomica.integrator.mcmove.MCMoveMolecule
moleculeSource - Variable in class etomica.models.hexane.MCMoveCBMC
moleculeSource - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
moleculeSource - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
moleculeSource - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
moleculeSource - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
moleculeSource - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
moleculeSource - Variable in class etomica.virial.MCMoveClusterAngleBend
moleculeSource - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
MoleculeSourceRandomDimer - Class in etomica.association
MoleculeSourceRandomDimer() - Constructor for class etomica.association.MoleculeSourceRandomDimer
MoleculeSourceRandomMolecule - Class in etomica.atom: MoleculeSource that returns a completely random molecule.
MoleculeSourceRandomMolecule() - Constructor for class etomica.atom.MoleculeSourceRandomMolecule
MoleculeSourceRandomMonomer - Class in etomica.association
MoleculeSourceRandomMonomer() - Constructor for class etomica.association.MoleculeSourceRandomMonomer
MoleculeToIndex - Interface in etomica.atom: Interface for class that associates an integer with an atom.
MoleculeToMoleculeList - Interface in etomica.atom: Interface for class that determines an AtomArrayList given an atom.
MoleculeToMoleculeListSpecies - Class in etomica.atom
MoleculeToMoleculeListSpecies(ISpecies) - Constructor for class etomica.atom.MoleculeToMoleculeListSpecies
MoleculeToMoleculeSetFixed - Class in etomica.atom
MoleculeToMoleculeSetFixed() - Constructor for class etomica.atom.MoleculeToMoleculeSetFixed
moleculeTotals - Variable in class etomica.box.AtomSetAllMolecules
moleFractionLeft - Variable in class etomica.modules.osmosis.Osmosis
moleFractionRight - Variable in class etomica.modules.osmosis.Osmosis
molIndex - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
molIndex - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
molNum - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
molSpeciesA - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
molSpeciesB - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
moment - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
moment - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
moment - Variable in class etomica.modules.droplet.MeterDeformation
moment - Variable in class etomica.modules.vle.VLESim
moment - Static variable in class etomica.potential.P2NitrogenHellmann
moment - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
moment - Variable in class etomica.species.SpeciesOriented
moment - Variable in class etomica.species.SpeciesSpheresRotatingMolecule
moment - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
moment0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
moment0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
moment1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
moment1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
momentj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
momentum - Variable in class etomica.action.BoxScaleMomenta
momentum - Variable in class etomica.integrator.IntegratorMD
monitorenergy - Static variable in class org.jmol.script.Token
monomer1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
monomerA - Variable in class etomica.action.IntegratorDimerApproach
monomerB - Variable in class etomica.action.IntegratorDimerApproach
monomerColor - Variable in class etomica.association.ColorSchemeSmer
monomerMonomerBondManager - Variable in class etomica.modules.colloid.ColloidSim
monomerMonomerBondManager - Variable in class etomica.modules.colloid.ConfigurationColloid
monomerMonomerBondManager - Variable in class etomica.modules.colloid.P1Wall
moreDefaultColors - Variable in class etomica.graphics.ColorSchemeByType
MOST_RECENT - Static variable in class etomica.data.AccumulatorAverage
MOST_RECENT - Static variable in class etomica.data.AccumulatorAverageBlockless
mostRecent - Variable in class etomica.data.AccumulatorAverage
mostRecent - Variable in class etomica.data.AccumulatorAverageBlockless
mostRecentBlock - Variable in class etomica.data.AccumulatorAverageFixed
mostRecentBlock - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
mostRecentValue - Variable in class etomica.normalmode.ModifierCells3D
mostRecentValue - Variable in class etomica.normalmode.ModifierXCells2D
mostRecentValue - Variable in class etomica.normalmode.ModifierYCells2D
MOUSE_NONE - Static variable in class org.jmol.viewer.JmolConstants
mouseClicked(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
mouseClicked(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
mouseClicked(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
mousedragfactor - Static variable in class org.jmol.script.Token
mouseEntered(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
mouseEntered(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
mouseEntered(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
MouseEventClusterPanel() - Constructor for class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
mouseExited(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
mouseExited(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
mouseExited(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
mousePressed(MouseEvent) - Method in class etomica.graphics.DisplayPlot.PopupListener
mousePressed(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
mousePressed(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
mousePressed(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
mouseReleased(MouseEvent) - Method in class etomica.graphics.DisplayPlot.PopupListener
mouseReleased(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
mouseReleased(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
mouseReleased(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
mousewheelfactor - Static variable in class org.jmol.script.Token
movable - Variable in class etomica.dimer.EnergyMap
movable - Variable in class etomica.dimer.SimDimerLJadatom
movable - Variable in class etomica.dimer.SimDimerLJgb
movable - Variable in class etomica.dimer.SimDimerMEAMadatom
movable - Variable in class etomica.dimer.SimDimerMEAMGB
movable - Variable in class etomica.kmc.SimKMCLJadatom
movable - Variable in class etomica.kmc.SimKMCMEAMadatom
movableAtoms - Variable in class etomica.dimer.IntegratorDimerMin
movableAtoms - Variable in class etomica.dimer.IntegratorDimerRT
movableSet - Variable in class etomica.dimer.SimDimerLJadatom
movableSet - Variable in class etomica.dimer.SimDimerMEAMadatom
movableSet - Variable in class etomica.dimer.SimDimerMEAMGB
movableSet - Variable in class etomica.kmc.SimKMCLJadatom
movableSet - Variable in class etomica.kmc.SimKMCMEAMadatom
movableSpecies - Variable in class etomica.dimer.IntegratorDimerMin
movableSpecies - Variable in class etomica.dimer.IntegratorDimerRT
move - Variable in class etomica.data.DataSourceAcceptanceRatio
move - Variable in class etomica.mappedvirial.MappedU
move - Variable in class etomica.mappedvirial.MappedVirialLJ
move - Variable in class etomica.mappedvirial.MappedVirialLJVGr
move - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
move - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
move - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
move - Variable in class etomica.modules.adsorption.ModifierPMu
move - Variable in class etomica.normalmode.HessianDB
move - Variable in class etomica.normalmode.SimOverlap
move - Variable in class etomica.normalmode.SimOverlapSoftSphere
move - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
move - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
move - Variable in class etomica.normalmode.SimOverlapSSnxy
move - Variable in class etomica.normalmode.SimUmbrella
move - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
moveA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
moveAction - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
moveB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
moved - Variable in class etomica.integrator.IntegratorVelocityVerletShake
moveEventManager - Variable in class etomica.integrator.IntegratorMC
moveHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
moveManager - Variable in class etomica.integrator.IntegratorManagerMC
moveManager - Variable in class etomica.integrator.IntegratorMC
moveMolecule - Variable in class etomica.AlkaneEH.CH4NVT
moveMolecule - Variable in class etomica.AlkaneEH.DHS_NVT
moveMolecule - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
moveMolecule - Variable in class etomica.dielectric.DHS_NVT
moveMolecule - Variable in class etomica.dielectric.DLJ_NVT_1site
moveMolecule - Variable in class etomica.dielectric.TIP4P_NVT
moveMolecule - Variable in class etomica.models.hexane.HexaneVolumeFraction
moveMolecule - Variable in class etomica.models.hexane.TestHexane
moveMolecule - Variable in class etomica.models.hexane.TestHexaneFileConfig
moveMolecule - Variable in class etomica.models.hexane.TestHexaneHarmonic
moveMolecule - Variable in class etomica.models.hexane.TestSetToUHexane
moveMoleculeAction - Variable in class etomica.association.BiasVolume2SiteAceticAcid
moveMoleculeAction - Variable in class etomica.association.BiasVolumeAceticAcid
moveMoleculeAction - Variable in class etomica.association.MCMoveBiasUBMolecule
moveMoleculeAction - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
moveMoleculeAction - Variable in class etomica.integrator.mcmove.MCMoveMolecule
moveMoleculeAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
moveMoleculeAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
moveMoleculeAction - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
moveMoleculeAction - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
moveTo(IVector) - Method in class etomica.math.geometry.Plane: Shifts the plane at fixed orientation so that it contains the given point.
moveto - Static variable in class org.jmol.script.Token
moveTracker - Variable in class etomica.integrator.mcmove.MCMove
moveWallAction - Variable in class etomica.modules.sam.SamGraphic
Mpi1ACell - Class in etomica.nbr.cell.molecule: Generates pairs that are cell-based neighbors of a specific Molecule.
Mpi1ACell(int, double, BoxAgentManager) - Constructor for class etomica.nbr.cell.molecule.Mpi1ACell: Constructor makes iterator that must have box specified and then be reset() before iteration.
MpiAACell - Class in etomica.nbr.cell.molecule: Returns iterates formed from all cell-based neighbor pairs.
MpiAACell(int, double, IBox) - Constructor for class etomica.nbr.cell.molecule.MpiAACell: Constructor makes iterator that must have box specified and then be reset() before iteration.
MpiInnerFixed - Class in etomica.atom.iterator: Pair iterator synthesized from two atom iterators, such that the inner-loop iteration is independent of the outer-loop atom.
MpiInnerFixed(MoleculeIterator, MoleculeIterator, boolean) - Constructor for class etomica.atom.iterator.MpiInnerFixed: Construct a pair iterator using the given atom iterators, indicating whether the atoms ordering in the AtomPair should be swapped from the default behavior.
MpiInnerVariable - Class in etomica.atom.iterator: Pair iterator synthesized from two atom iterators, such that the inner-loop iteration depends on the outer-loop atom.
MpiInnerVariable(MoleculeIterator, MoleculeIteratorMoleculeDependent, boolean) - Constructor for class etomica.atom.iterator.MpiInnerVariable: Construct a pair iterator using the given atom iterators, indicating whether the atoms ordering in the AtomPair should be swapped from the default behavior.
MpiInterArrayList - Class in etomica.atom.iterator: Returns all pairs formed from two different untabbed lists of molecules.
MpiInterArrayList() - Constructor for class etomica.atom.iterator.MpiInterArrayList: Construct iterator with an empty lists.
MpiInterArrayList(IMoleculeList, IMoleculeList) - Constructor for class etomica.atom.iterator.MpiInterArrayList: Constructs iterator to return pairs from the given lists.
MpiInterspecies1A - Class in etomica.atom.iterator: Gives pairs formed from the molecules of two different species in a box, taking one molecule of one species with all molecules of the other.
MpiInterspecies1A(ISpecies[]) - Constructor for class etomica.atom.iterator.MpiInterspecies1A: Sorts given array of species according to species index, then constructs iterator such that atom0 of the pair iterates is in (sorted) species[0], and atom1 is in (sorted) species[1], regardless of which is specified via setTarget.
MpiInterspeciesAA - Class in etomica.atom.iterator: Gives pairs formed from the molecules of two different species in a box.
MpiInterspeciesAA(ISpecies[]) - Constructor for class etomica.atom.iterator.MpiInterspeciesAA: Constructs iterator that provides iterates taken from the molecules of two species.
MpiIntraArrayList - Class in etomica.atom.iterator: Returns all pairs formed from a single list of molecules.
MpiIntraArrayList() - Constructor for class etomica.atom.iterator.MpiIntraArrayList: Construct iterator with an empty list.
MpiIntraArrayList(IMoleculeList) - Constructor for class etomica.atom.iterator.MpiIntraArrayList: Constructs iterator to return pairs from the given list.
MpiIntraspecies1A - Class in etomica.atom.iterator: Gives pairs formed from the molecules of a species in a box, taking one molecule the species with all of its other molecules.
MpiIntraspecies1A(ISpecies) - Constructor for class etomica.atom.iterator.MpiIntraspecies1A
MpiIntraspecies1A(ISpecies, MoleculeToMoleculeListSpecies) - Constructor for class etomica.atom.iterator.MpiIntraspecies1A
MpiIntraspeciesAA - Class in etomica.atom.iterator: Gives pairs formed from the molecules of a single species in a box.
MpiIntraspeciesAA(ISpecies) - Constructor for class etomica.atom.iterator.MpiIntraspeciesAA
MpiMolecule - Class in etomica.atom.iterator: Adapater class that wraps three atomPair iterators, one suitable for iterating over all molecule pairs in a box (AA), another suitable for iterating over all molecule pairs formed with a target molecule (1A), and the third suitable for iterating over a single molecule pair (11).
MpiMolecule(MoleculesetIteratorPDT, MoleculesetIteratorBoxDependent) - Constructor for class etomica.atom.iterator.MpiMolecule: Constructs iterator by wrapping three others.
mReeHooverFactor - Variable in class etomica.virial.cluster.ClusterDiagram
mrqcof(double[]) - Method in class etomica.util.numerical.NonLinearCurveDiffFitting
mrqcof(double[]) - Method in class etomica.util.numerical.NonLinearCurveFitting
mrqcofA(double[]) - Method in class etomica.util.numerical.NonLinearCurveDiffFitting
mrqcofA(double[]) - Method in class etomica.util.numerical.NonLinearCurveFitting
mrqmin() - Method in class etomica.util.numerical.NonLinearCurveDiffFitting
mrqmin() - Method in class etomica.util.numerical.NonLinearCurveFitting
msdCalc(MeterMeanSquareDisplacement) - Method in class etomica.kmc.IntegratorKMCCluster
MSDCoordWriter - Class in etomica.zeolite
MSDCoordWriter(ISpace, String) - Constructor for class etomica.zeolite.MSDCoordWriter
MSDProcessor - Class in etomica.zeolite
MSDProcessor(ISpace, String, String) - Constructor for class etomica.zeolite.MSDProcessor
mspMinus - Variable in class etomica.virial.PYGenerator.IteratorEF
mspPlus - Variable in class etomica.virial.PYGenerator.IteratorEF
mSquare - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
mSquare - Variable in class etomica.dielectric.TIP4P_NVT.Param
mt - Variable in class etomica.util.RandomMersenneTwister
mti - Variable in class etomica.util.RandomMersenneTwister
mType - Variable in class etomica.models.water.SpeciesWater4P
mType - Variable in class etomica.models.water.SpeciesWater4PCOM
mType - Variable in class etomica.models.water.SpeciesWater4POriented
mu - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
mu - Variable in class etomica.metastable.LJmuVT.LJMCParams
mu - Variable in class etomica.models.co2.PNCO2GCPM
mu - Variable in class etomica.models.co2.PNGCPM
mu(double) - Method in class etomica.modules.adsorption.EOSSW
mu(double) - Method in class etomica.modules.adsorption.EOSSWPatel
mu(double) - Method in class etomica.modules.adsorption.VEOS3SW
Mu - Class in etomica.modules.mu
Mu(ISpace) - Constructor for class etomica.modules.mu.Mu
mu - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
mu - Variable in class etomica.normalmode.SimLJVacancy.LJParams
mu - Variable in class etomica.statmech.HardSphereSolid.EOSParams
mu0 - Variable in class etomica.metastable.LJmuVT.LJMCParams
Mu1Modulator() - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
mu2 - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
mu2 - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
Mu2Modulator() - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
MuFGeneral - Class in etomica.virial
MuFGeneral(double, IPotentialMolecular) - Constructor for class etomica.virial.MuFGeneral
muForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
muForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
muForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
MuGeneral - Class in etomica.virial
MuGeneral(double, IPotentialMolecular) - Constructor for class etomica.virial.MuGeneral
MuGraphic - Class in etomica.modules.mu
MuGraphic(Mu, ISpace) - Constructor for class etomica.modules.mu.MuGraphic
MuGraphic.Applet - Class in etomica.modules.mu
MuGraphic.DataProcessorMu - Class in etomica.modules.mu
MuGraphic.DataSinkExcludeOverlap - Class in etomica.modules.mu
MuGraphic.ModifierAtomDiameter - Class in etomica.modules.mu
MuGraphic.ModifierEpsilon - Class in etomica.modules.mu
MuGraphic.ModifierLambda - Class in etomica.modules.mu
muHistory - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
Mul - Class in etomica.graph.operations
Mul() - Constructor for class etomica.graph.operations.Mul
Mul(double[], double[]) - Static method in class etomica.virial.CalcFFT
mul(Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(float) - Method in class org.jmol.util.Matrix4f: Multiplies each element of this matrix by a scalar.
mul(Matrix4f) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(float) - Method in class org.jmol.util.Quaternion
Mul.MulParameters - Class in etomica.graph.operations
mul2(Matrix3f, Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the result of multiplying the two argument matrices together.
mul2(Matrix4f, Matrix4f) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to the result of multiplying the two argument matrices together.
mulf(float) - Method in class org.jmol.util.Matrix3f: Multiplies each element of this matrix by a scalar.
mulFlex - Variable in class etomica.graph.operations.BiComponentSubst
mulFlex - Variable in class etomica.graph.operations.ComponentSubst
mulFlex - Variable in class etomica.graph.operations.Unfactor
MulFlexible - Class in etomica.graph.operations: Perform graph multiplication for flexible molecules.
MulFlexible() - Constructor for class etomica.graph.operations.MulFlexible
MulFlexible.MulFlexibleParameters - Class in etomica.graph.operations
MulFlexibleParameters(char[], byte, byte, byte, boolean) - Constructor for class etomica.graph.operations.MulFlexible.MulFlexibleParameters
mulParameters() - Method in class etomica.graph.operations.ConvParameters
MulParameters(byte) - Constructor for class etomica.graph.operations.Mul.MulParameters
mulQ(Quaternion) - Method in class org.jmol.util.Quaternion
mulScalar - Variable in class etomica.graph.operations.BiComponentSubst
mulScalar - Variable in class etomica.graph.operations.ComponentSubst
MulScalar - Class in etomica.graph.operations: Multiply graphs by a scalar (coefficient)
MulScalar() - Constructor for class etomica.graph.operations.MulScalar
mulScalar - Variable in class etomica.virial.PYGenerator.IteratorEF
MulScalarParameters - Class in etomica.graph.operations
MulScalarParameters(int, int) - Constructor for class etomica.graph.operations.MulScalarParameters
MulScalarParameters(Coefficient) - Constructor for class etomica.graph.operations.MulScalarParameters
multGcdLcm(Ifactor, int) - Method in class etomica.veos.bigdecimal.Ifactor: Multiply with another positive integer.
multibody - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
multibody - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
multibody - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
multibody - Variable in class etomica.virial.cluster.VirialDiagrams
multibody - Variable in class etomica.virial.cluster.VirialDiagramsMix
multibody - Variable in class etomica.virial.cluster.VirialDiagramsPT
multibody - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
multibody - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JmolConstants
MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JmolConstants
MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JmolConstants
MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JmolConstants
multiBonds - Variable in class etomica.virial.ClusterBondsNonAdditive
Multiharmonic - Class in etomica.modules.multiharmonic: TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates
Multiharmonic() - Constructor for class etomica.modules.multiharmonic.Multiharmonic
MultiharmonicGraphic - Class in etomica.modules.multiharmonic
MultiharmonicGraphic(Multiharmonic, ISpace) - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphic
MultiharmonicGraphic.Applet - Class in etomica.modules.multiharmonic
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphicMC
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC(MultiharmonicMC, ISpace) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC.DataProcessAHT - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSinkReweightedDeltaU - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceAlphaAlpha - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceAlphaAlpha - Class in etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.umbrella
MultiharmonicGraphicMC.DataSourceAlphaFE - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceBias - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceChiSlope - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceFE - Class in etomica.modules.multiharmonic.mbar
MultiharmonicGraphicMC.DataSourceFunctionRaw - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceUa - Class in etomica.modules.multiharmonic.overlap
MultiharmonicGraphicMC.DataSourceUa2 - Class in etomica.modules.multiharmonic.overlap
MultiharmonicMC - Class in etomica.modules.multiharmonic.mbar: MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicMC
MultiharmonicMC - Class in etomica.modules.multiharmonic: MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.MultiharmonicMC
MultiharmonicMC - Class in etomica.modules.multiharmonic.overlap: MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicMC
MultiharmonicMC - Class in etomica.modules.multiharmonic.umbrella: MC version of multi-harmonic simulation.
MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
multiP - Variable in class etomica.virial.cluster.VirialDiagramsMix
multiplebondradiusfactor - Static variable in class org.jmol.script.Token
multiplebondspacing - Static variable in class org.jmol.script.Token
multiply(Coefficient) - Method in interface etomica.graph.model.Coefficient
multiply(Coefficient) - Method in class etomica.graph.model.impl.CoefficientImpl
multiply(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Multiply by a constant factor.
multiply(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Multiply by another polynomial
multiply(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd: Multiply by another square root.
multiply(Rational) - Method in class etomica.veos.bigdecimal.BigSurd: Multiply by a rational number.
multiply(BigInteger) - Method in class etomica.veos.bigdecimal.BigSurd: Multiply by a BigInteger.
multiply(int) - Method in class etomica.veos.bigdecimal.BigSurd: Multiply by an integer.
multiply(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec: Multiply by another square root.
multiply(BigInteger) - Method in class etomica.veos.bigdecimal.Ifactor: Multiply with another positive integer.
multiply(int) - Method in class etomica.veos.bigdecimal.Ifactor: Multiply with another positive integer.
multiply(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor: Multiply with another positive integer.
multiply(Rational) - Method in class etomica.veos.bigdecimal.Rational: Multiply by another fraction.
multiply(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Multiply by a BigInteger.
multiply(int) - Method in class etomica.veos.bigdecimal.Rational: Multiply by an integer.
Multiply(Set<Graph>, Set<Graph>) - Static method in class etomica.virial.IEGenerator
multiplyRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Multiply and round.
multiplyRound(BigComplex, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Multiply and round.
multiplyRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Multiply and round.
multiplyRound(BigDecimal, Rational) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Multiply and round.
multiplyRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Multiply and round.
multiplyRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Multiply and round.
multiprocessor - Static variable in class org.jmol.script.Token
multiTol - Variable in class etomica.virial.ClusterWheatleyMultibody
MulUnion - Class in etomica.graph.operations: This operation multiplies two graphs (or each pair of graphs from two sets) by superimposing all points (with the idea that all nodes are distinguishable).
MulUnion() - Constructor for class etomica.graph.operations.MulUnion
mUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
mUnit - Variable in class etomica.modules.swmd.SwmdGraphic
muProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
Mv1Squared(IVector) - Method in interface etomica.api.IVector: Returns square of vector resulting from subtracting given vector from this one.
Mv1Squared(IVector) - Method in class etomica.space1d.Vector1D
Mv1Squared(IVector) - Method in class etomica.space2d.Vector2D
Mv1Squared(IVector) - Method in class etomica.space3d.Vector3D
Mv1Squared(IVector) - Method in class etomica.spaceNd.VectorND
mxcBond - Variable in class etomica.virial.cluster.VirialDiagrams
MxcBond - Variable in class etomica.virial.cluster.VirialDiagrams
mxcBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
MxcBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
mxter - Static variable in class etomica.potential.P2O2Bartolomei
myAcceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
myAcceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
myAcceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
MyAgent(ISpace) - Constructor for class etomica.integrator.IntegratorVelocityVerlet.MyAgent
MyAgent(ISpace) - Constructor for class etomica.modules.droplet.IntegratorDroplet.MyAgent
MyAgent(ISpace) - Constructor for class etomica.normalmode.HSNPT.MyAgent
MyAgent(double, double) - Constructor for class etomica.potential.P3AxilrodTeller.MyAgent
MyAgent(double[], IVector[], double[], IVector[]) - Constructor for class etomica.potential.P3Induction.MyAgent
MyAgentSource(ISpace) - Constructor for class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
MyAgentSource(ISpace) - Constructor for class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
MyApplet - Class in etomica.modules.clustergenerator
MyApplet() - Constructor for class etomica.modules.clustergenerator.MyApplet
MyApplet.BondInteractionTypeToggler - Class in etomica.modules.clustergenerator: Options for type of bond-interaction (e-bonds, f-bonds, etc)
MyApplet.BondTypeToggler - Class in etomica.modules.clustergenerator: Options for type of bond array
MyApplet.ComponentEventMyPanel - Class in etomica.modules.clustergenerator: This class is to be notified to graphicOut2 when the window of applet is resized
MyApplet.ConnectedToggler - Class in etomica.modules.clustergenerator
MyApplet.GraphicsToggler - Class in etomica.modules.clustergenerator
MyApplet.MouseEventClusterPanel - Class in etomica.modules.clustergenerator: This class is for showing bonds of selected cluster in GraphicPanel
MyApplet.NumbersToggler - Class in etomica.modules.clustergenerator: Options for showing index of particle or not
MyApplet.PointsToggler - Class in etomica.modules.clustergenerator: Option of showing particles or not
MyApplet.ReeHooverToggler - Class in etomica.modules.clustergenerator: Options for type of bond-interaction (e-bonds, f-bonds, etc)
MyApplet.Starter - Class in etomica.modules.clustergenerator
MyApplet.Stopper - Class in etomica.modules.clustergenerator
myAtom - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
myAtom - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
myAtoms - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
myAtoms - Variable in class etomica.virial.MCMoveClusterRingRegrow
myAtoms - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
myAtoms - Variable in class etomica.virial.MCMoveClusterRingScale
MyBigDecimal - Class in etomica.veos: Data class to handle operations involving large numbers.
MyBigDecimal() - Constructor for class etomica.veos.MyBigDecimal: Default constructor sets value to 0.0
MyBigDecimal(double) - Constructor for class etomica.veos.MyBigDecimal: Constructs using the given value.
MyBigDecimal(IBigValue) - Constructor for class etomica.veos.MyBigDecimal: Copy constructor.
MyBigDecimal(BigDecimal) - Constructor for class etomica.veos.MyBigDecimal
myCharge - Variable in class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
myCharge - Variable in class etomica.models.water.ChargeAgentSourceTIP4PWater
myCharge - Variable in class etomica.paracetamol.ChargeAgentSourceParacetamol
MyCharge(double) - Constructor for class etomica.potential.EwaldSummation.MyCharge
MyCharge(double) - Constructor for class etomica.potential.EwaldSumMolecules.MyCharge
myData - Variable in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
myData - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
myData - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
myData - Variable in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
MyData() - Constructor for class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
MyData() - Constructor for class etomica.virial.MeterVirialBinMultiThreaded.MyData
MyData(int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded.MyData
MyDataCov(int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
MyEigenvalueDecomposition - Class in etomica.eigenstuff: Eigenvalues and eigenvectors of a real matrix.
MyEigenvalueDecomposition(int, double[][]) - Constructor for class etomica.eigenstuff.MyEigenvalueDecomposition: Check for symmetry, then construct the eigenvalue decomposition
myEllipse3D - Variable in class g3dsys.images.Ellipse
MyEventManager() - Constructor for class etomica.graphics.DeviceTernarySelector.MyEventManager
myIds - Static variable in class etomica.virial.cluster.VirialDiagrams
myImage - Variable in class etomica.util.Grabber.ImagePanel
myLat - Variable in class etomica.config.ConfigurationLattice
myLat - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
myLat - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
MyLattice(SpaceLattice, IVector, IVector) - Constructor for class etomica.config.ConfigurationLattice.MyLattice
MyLattice(SpaceLattice, IVectorMutable, IVectorMutable) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
MyLattice(SpaceLattice, IVectorMutable, IVectorMutable) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
myListener - Variable in class etomica.util.Grabber.ActionCornerSetter
MyMCMove - Class in etomica.modules.adsorption
MyMCMove(IntegratorBox, IRandom, ISpace, double, double, int) - Constructor for class etomica.modules.adsorption.MyMCMove: Constructor for MyMCMove.
MyMCMove - Class in etomica.modules.dcvgcmd
MyMCMove(IntegratorBox, IRandom, ISpace, double) - Constructor for class etomica.modules.dcvgcmd.MyMCMove: Constructor for MyMCMove.
myMoleculeIndices - Variable in class etomica.virial.MayerFunctionThreeBody
myPanel - Variable in class etomica.modules.clustergenerator.MyApplet
myRejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
mySeeds - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
mySeeds - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
MySpeciesEditor(SpeciesSpheresMono, String) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor
mysum - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
MyTypeAgent(OrientationCalcQuaternion) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion.MyTypeAgent
MyWall() - Constructor for class etomica.modules.osmosis.Osmosis.MyWall

N

N - Variable in class etomica.dimer.IntegratorDimerMin
N - Variable in class etomica.dimer.IntegratorDimerRT
n - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
n - Variable in class etomica.meam.PotentialFeEAM
n - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
N - Static variable in class etomica.potential.P3HydrogenManzhos
n - Variable in class etomica.potential.P4TorsionDreiding
N - Variable in class etomica.util.numerical.FittingFunctionNonLinear
n - Variable in class etomica.util.numerical.PadeApproximation.VirialParam
N - Static variable in class etomica.util.RandomMersenneTwister
n - Variable in class etomica.veos.bigdecimal.Ifactor: The standard representation of the number
n - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
N - Variable in class etomica.virial.CalcFFT
n - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
n - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
n - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
n - Variable in class etomica.virial.cluster.VirialDiagrams
n - Variable in class etomica.virial.cluster.VirialDiagramsMix
n - Variable in class etomica.virial.cluster.VirialDiagramsMix2
n - Variable in class etomica.virial.cluster.VirialDiagramsPT
n - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
n - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
n - Variable in class etomica.virial.ClusterChainHS
n - Variable in class etomica.virial.ClusterChainSoft
n - Variable in class etomica.virial.ClusterSinglyConnected
n - Variable in class etomica.virial.ClusterSumHS
n - Variable in class etomica.virial.ClusterWheatleyExtendSW
n - Variable in class etomica.virial.ClusterWheatleyHS
n - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
n - Variable in class etomica.virial.ClusterWheatleySoft
n - Variable in class etomica.virial.ClusterWheatleySoftBD
n - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
n - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
n - Variable in class etomica.virial.MeterVirialSWWE
n - Variable in class etomica.virial.simulations.ReeHooverMC.VirialParam
n0 - Variable in class etomica.potential.P2HydrogenHinde
n0 - Variable in class etomica.potential.P2HydrogenHindeAtomic
n0 - Variable in class etomica.potential.P2HydrogenHindePatkowski
n0 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
n0 - Variable in class etomica.potential.P2HydrogenPatkowski
n0 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
N1 - Variable in class etomica.dimer.IntegratorDimerRT
n1 - Variable in class etomica.graph.isomorphism.AbstractSearchState
n1 - Variable in class etomica.potential.P2HydrogenHinde
n1 - Variable in class etomica.potential.P2HydrogenHindeAtomic
n1 - Variable in class etomica.potential.P2HydrogenHindePatkowski
n1 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
n1 - Variable in class etomica.potential.P2HydrogenPatkowski
n1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
n2 - Variable in class etomica.graph.isomorphism.AbstractSearchState
N_BASE - Static variable in class etomica.units.Dimension: Number of base dimensions, equal to seven.
n_max - Static variable in class etomica.potential.P2HydrogenPatkowski
n_max - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
n_min - Static variable in class etomica.potential.P2HydrogenPatkowski
n_min - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
nA - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
nA - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
nA - Variable in class etomica.normalmode.NormalModes1DHR
Na - Static variable in class etomica.potential.P2QChemInterpolated
naamax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nAccBlocks - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
nAccBlocks - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
nAccBlocks - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
nAccept - Variable in class etomica.integrator.mcmove.MCMoveTracker
nAccepted - Variable in class etomica.integrator.IntegratorMD
nAccepted - Variable in class etomica.util.numerical.AkimaSplineSmoother
nada - Static variable in class org.jmol.script.Token
nAlpha - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
name - Variable in class etomica.compatibility.Feature
name - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
nameOf(int) - Static method in class org.jmol.script.Token: note: nameOf is a very inefficient mechanism for getting the name of a token.
names - Static variable in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
nand(Bitmap) - Method in interface etomica.graph.model.Bitmap: Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap = ~(bitmap & other).
nand(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
nand(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1) for a compatible instance.
nand(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
NANO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-9.
nAtoms - Variable in class etomica.association.MCMoveVolumeAssociated.Agent
nAtoms - Variable in class etomica.data.meter.MeterProfileByAtoms
nAtoms - Variable in class etomica.modules.render.ParseObj
nAtoms - Variable in class etomica.simulation.prototypes.HSMD3D.HSMD3DParam
nAtomTypes - Variable in class etomica.models.co2.PNGCPM
nAttempt - Variable in class etomica.util.numerical.AkimaSplineSmoother
nAttempts - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
navfps - Static variable in class org.jmol.script.Token
navigate - Static variable in class org.jmol.script.Token
navigatesurface - Static variable in class org.jmol.script.Token
navigationdepth - Static variable in class org.jmol.script.Token
navigationmode - Static variable in class org.jmol.script.Token
navigationperiodic - Static variable in class org.jmol.script.Token
navigationslab - Static variable in class org.jmol.script.Token
navigationspeed - Static variable in class org.jmol.script.Token
navx - Static variable in class org.jmol.script.Token
navy - Static variable in class org.jmol.script.Token
NAVY - Static variable in class org.jmol.util.Colix
navz - Static variable in class org.jmol.script.Token
nBasis - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
nBasis - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
nBasis - Variable in class etomica.normalmode.MeterSolidPropsLJ
nbbmax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nBeads - Variable in class etomica.virial.simulations.ModifierTPI
nBeads - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
nBeads - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
nBeads - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
nBeads - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
nBeads - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
nBeads - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
nBeads - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
nBeads - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
nBeads - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
nbin - Static variable in class etomica.math.SpecialFunctions: Returns the Wigner 3j symbol associated with coupling angular momenta in quantum mechanics.
nbin - Static variable in class etomica.potential.P2O2Bartolomei
nbins - Variable in class etomica.mappedvirial.MappedUpotential
nbins - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
nbins - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
nBins - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
nBins - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
nBins - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
nBins - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
nBins - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
nBins - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
nBins - Variable in class etomica.util.HistogramNotSoSimple
nBins - Variable in class etomica.util.HistogramReweightedData
nBins - Variable in class etomica.util.HistogramSimple
nBlocks - Variable in class etomica.mappedvirial.MappedU.LJMDParams
nBlocks - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
nBlocks - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
nBody() - Method in interface etomica.api.IPotential: The number of atoms on which the potential depends.
nBody - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
nBody - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
nBody - Variable in class etomica.atom.iterator.ANIntergroupCoupled
nBody() - Method in class etomica.atom.iterator.ANIntergroupCoupled
nBody() - Method in class etomica.atom.iterator.ANIntergroupExchange
nBody - Variable in class etomica.atom.iterator.ANIntragroupExchange
nBody() - Method in class etomica.atom.iterator.ANIntragroupExchange
nBody() - Method in class etomica.atom.iterator.ApiIndexList: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.atom.iterator.ApiInnerVariable
nBody() - Method in class etomica.atom.iterator.ApiInterArrayList: Returns 2, indicating that this is a pair iterator
nBody() - Method in class etomica.atom.iterator.ApiIntergroup
nBody() - Method in class etomica.atom.iterator.ApiIntraArrayList: Returns 2, indicating that this is a pair iterator
nBody() - Method in class etomica.atom.iterator.ApiIntragroup
nBody() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
nBody() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Returns 1, indicating that this is an atom AtomSet iterator.
nBody() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Returns 1, indicating that this is an atom iterator.
nBody() - Method in class etomica.atom.iterator.AtomIteratorNull
nBody() - Method in class etomica.atom.iterator.AtomIteratorSinglet
nBody() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList: Returns 3, indicating that this is a set of three iterator.
nBody() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList: Returns 4, indicating that this is a set of four iterator.
nBody() - Method in interface etomica.atom.iterator.AtomsetIterator: Returns the number of atoms given in each iterate, i.e., the size of the atom array returned with each call to next().
nBody() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
nBody() - Method in class etomica.atom.iterator.MoleculeIteratorAll
nBody() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Returns 1, indicating that this is an atom iterator.
nBody() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet
nBody() - Method in class etomica.atom.iterator.MpiInnerFixed
nBody() - Method in class etomica.atom.iterator.MpiInnerVariable
nBody() - Method in class etomica.atom.iterator.MpiInterArrayList: Returns 2, indicating that this is a pair iterator
nBody() - Method in class etomica.atom.iterator.MpiInterspecies1A
nBody() - Method in class etomica.atom.iterator.MpiInterspeciesAA: Returns 2, indicating that this is a pair iterator
nBody() - Method in class etomica.atom.iterator.MpiIntraArrayList: Returns 2, indicating that this is a pair iterator
nBody() - Method in class etomica.atom.iterator.MpiIntraspecies1A
nBody() - Method in class etomica.atom.iterator.MpiIntraspeciesAA: Returns 2, indicating that this is a pair iterator
nBody() - Method in class etomica.atom.iterator.MpiMolecule: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.atom.iterator.TripletInnerSequential
nBody() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
nBody() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
nBody() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
nBody() - Method in class etomica.models.co2.P2CO2H2OWheatley
nBody() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
nBody() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
nBody() - Method in class etomica.models.co2.P2CO2Hellmann
nBody() - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
nBody() - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
nBody() - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
nBody() - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
nBody() - Method in class etomica.models.water.P2WaterSzalewicz
nBody() - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
nBody() - Method in class etomica.modules.adsorption.P1Wall
nBody - Variable in class etomica.modules.clustergenerator.MyApplet
nBody() - Method in class etomica.modules.colloid.P1Wall
nBody() - Method in class etomica.modules.droplet.P1Smash
nBody() - Method in class etomica.modules.materialfracture.P1Tension
nBody() - Method in class etomica.modules.sam.P1Sinusoidal
nBody() - Method in class etomica.nbr.cell.Api1ACell: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.nbr.cell.ApiAACell: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.nbr.cell.AtomIteratorCell: Returns 1, indicating that this is an atom iterator.
nBody() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell: Returns 1, indicating that this is an atom iterator.
nBody() - Method in class etomica.nbr.cell.molecule.Mpi1ACell: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.nbr.cell.molecule.MpiAACell: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.nbr.site.Api1ASite: Returns 2, indicating that this is a pair iterator.
nBody() - Method in class etomica.normalmode.P1ConstraintNbr
nBody() - Method in class etomica.normalmode.P1ConstraintNbrHcp
nBody() - Method in class etomica.potential.EwaldSummation
nBody() - Method in class etomica.potential.EwaldSummation.P2EwaldReal
nBody() - Method in class etomica.potential.EwaldSumMolecules
nBody() - Method in class etomica.potential.P1HardBoundary
nBody() - Method in class etomica.potential.P1HydrogenMielke
nBody() - Method in class etomica.potential.P1HydrogenMielke.P2HydrogenMielkeAtomic
nBody() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
nBody() - Method in class etomica.potential.P2EffectiveFeynmanHibbs
nBody() - Method in class etomica.potential.P2HardWrapper
nBody() - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
nBody() - Method in class etomica.potential.P2HePCKLJS.P2HeTI
nBody() - Method in class etomica.potential.P2HeSimplified.P2HeQFH
nBody() - Method in class etomica.potential.P2HeSimplified.P2HeTI
nBody() - Method in class etomica.potential.P2HydrogenHinde
nBody() - Method in class etomica.potential.P2HydrogenHindeAtomic
nBody() - Method in class etomica.potential.P2HydrogenHindePatkowski
nBody() - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
nBody() - Method in class etomica.potential.P2HydrogenPatkowski
nBody() - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
nBody() - Method in class etomica.potential.P2MoleculeMonatomic
nBody() - Method in class etomica.potential.P2NitrogenHellmann
nBody() - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
nBody() - Method in class etomica.potential.P2O2Bartolomei
nBody() - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
nBody() - Method in class etomica.potential.P2SemiclassicalAtomic
nBody() - Method in class etomica.potential.P2SemiclassicalMolecular
nBody() - Method in class etomica.potential.P2WaterPotentialsJankowski
nBody() - Method in class etomica.potential.P3AxilrodTeller
nBody() - Method in class etomica.potential.P3HydrogenATM
nBody() - Method in class etomica.potential.P3HydrogenManzhos
nBody() - Method in class etomica.potential.P3Induction
nBody() - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
nBody() - Method in class etomica.potential.Potential: The number of atoms on which the potential depends.
nBody() - Method in class etomica.potential.PotentialAtomicSum
nBody() - Method in class etomica.potential.PotentialMaster.AtomIterator0
nBody() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
nBody - Variable in class etomica.potential.PotentialMolecular
nBody() - Method in class etomica.potential.PotentialMolecular: The number of atoms on which the potential depends.
nBody() - Method in class etomica.potential.PotentialMolecularSum
nBody() - Method in class etomica.virial.P1IntraLambda
nBody - Variable in class etomica.virial.PotentialCommonAtomic
nBody() - Method in class etomica.virial.PotentialCommonAtomic
nBody() - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
nBody() - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
nBody - Variable in class etomica.virial.PotentialNonAdditive
nBody() - Method in class etomica.virial.PotentialNonAdditive
nBody() - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
nBody - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
nBody - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
nBodyField - Variable in class etomica.modules.clustergenerator.MyApplet
nBodyPretend - Variable in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
nbrDistance - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
nbrDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
nbrList - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
nbrs - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
nbrVectors - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
nC - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
nC - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
nC - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
nC - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
nC - Variable in class etomica.normalmode.NormalModesMolecular
nC - Variable in class etomica.virial.ClusterChainHS
nC - Variable in class etomica.virial.ClusterChainSoft
nCell - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
nCell - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
nCell - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
nCell - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
nCellNum - Variable in class etomica.normalmode.NormalModes3D
nCells - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
nCells - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
nCells - Variable in class etomica.normalmode.HessianDB
nCells - Variable in class etomica.normalmode.LJVacancyMin
nCells - Variable in class etomica.normalmode.MeterSolidPropsLJ
nCells - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
nCells - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
nCells - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
nCells - Variable in class etomica.normalmode.SimBennet
nCells - Variable in class etomica.normalmode.SimCalcSLJ
nCells - Variable in class etomica.normalmode.SimCalcSMorse
nCells - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
nCells - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
nCells - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
nCells - Variable in class etomica.normalmode.SimEinStep1
nCells - Variable in class etomica.normalmode.SimEinStep1HCP
nCells - Variable in class etomica.normalmode.SimEinStep2
nCells - Variable in class etomica.normalmode.SimEinStep2HCP
nCells - Variable in class etomica.normalmode.SimHarmonic
nCells - Variable in class etomica.normalmode.SimHarmonicUmbrella
nCells - Variable in class etomica.normalmode.SimLJHTTISuper
nCells - Variable in class etomica.normalmode.SimLJHTTISuperHCP
nCells - Variable in class etomica.normalmode.SimOverlap
nCells - Variable in class etomica.normalmode.SimOverlapLJ
nCells - Variable in class etomica.normalmode.SimOverlapLJModule
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphere
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
nCells - Variable in class etomica.normalmode.SimOverlapSSnxy
nCells - Variable in class etomica.normalmode.SimTargetUmbrella
nCells - Variable in class etomica.normalmode.SimUmbrella
nCells - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
nCellsX - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
nCellsX - Variable in class etomica.modules.sam.ConfigurationSAM
nCellsZ - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
nCellsZ - Variable in class etomica.modules.sam.ConfigurationSAM
nci - Static variable in class org.jmol.script.Token
nCO - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
nColumns - Variable in class etomica.graphics.DisplayTable
nColumnsA - Variable in class etomica.normalmode.MeterSolidPropsLJ
ncom - Variable in class etomica.util.numerical.Function1d
nComp1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
nComp1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nComp2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
nComp2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
NCopy - Class in etomica.graph.operations
NCopy() - Constructor for class etomica.graph.operations.NCopy
nCrossLinkersAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
nCutoffs - Variable in class etomica.liquidLJ.DataProcessorReweight
nCutoffs - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
nData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
nData - Variable in class etomica.data.AccumulatorHistory
nData - Variable in class etomica.data.DataHistogram
nData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
ndata - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
ndata - Variable in class etomica.util.numerical.NonLinearCurveFitting
nDataInfo - Variable in class etomica.data.AccumulatorAverageCollapsingLog
nDataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
nDataSource - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
NDelta - Variable in class etomica.dimer.IntegratorDimerMin
NDelta - Variable in class etomica.dimer.IntegratorDimerRT
nDiAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
nDimension() - Method in class etomica.units.DimensionRatio
nDiol - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
nEachIndices - Variable in class etomica.virial.cluster.PermutationIterator
nEachIndicesCheck - Variable in class etomica.virial.cluster.PermutationIterator
Near() - Constructor for class etomica.virial.MeterVirialExternalFieldSW.Near
nearestImage(IVectorMutable) - Method in interface etomica.api.IBoundary: The nearest image is the pair of atom images that are closest when all periodic-boundary images are considered.
nearestImage(IVectorMutable) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
nearestImage(IVectorMutable) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
nearestImage(IVectorMutable) - Method in class etomica.space.BoundaryDeformablePeriodic
nearestImage(IVectorMutable) - Method in class etomica.space.BoundaryRectangularNonperiodic: Does nothing.
nearestImage(IVectorMutable) - Method in class etomica.space.BoundaryRectangularPeriodic
nearestImage(IVectorMutable) - Method in class etomica.space.BoundaryRectangularPore
nearestImage(IVectorMutable) - Method in class etomica.space.BoundaryRectangularSlit
nearestImage(IVectorMutable) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
needNeighborUpdate - Variable in class etomica.lattice.RectangularLatticeNbrIterator
needSetupIterators - Variable in class etomica.atom.iterator.ANIntergroupCoupled
needSetupIterators - Variable in class etomica.atom.iterator.ANIntergroupExchange
needSetupIterators - Variable in class etomica.atom.iterator.ANIntragroupExchange
needSetupIterators - Variable in class etomica.atom.iterator.ApiIntergroup
needUpdate - Variable in class etomica.graphics.EtomicaPlot
needUpdate(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
needUpdate(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
needUpdate(IAtom) - Method in class etomica.modules.sam.CriterionTether3
needUpdate(IAtom) - Method in class etomica.nbr.CriterionAdapter: Indicates whether the neighbor list for the given atom should be updated, according to the wrapped criterion.
needUpdate(IAtom) - Method in class etomica.nbr.CriterionAll: Always returns false, indicating that neighbor list never needs updating.
needUpdate(IAtom) - Method in class etomica.nbr.CriterionNone: Always returns false, indicating that neighbor list never needs updating.
needUpdate(IAtom) - Method in class etomica.nbr.CriterionPositionWall
needUpdate(IAtom) - Method in class etomica.nbr.CriterionSimple
needUpdate(IMolecule) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular: Indicates whether the neighbor list for the given atom should be updated, according to the wrapped criterion.
needUpdate(IMolecule) - Method in class etomica.nbr.molecule.CriterionAllMolecular: Always returns false, indicating that neighbor list never needs updating.
needUpdate(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
needUpdate(IMolecule) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular: Indicates whether the neighbor list for the given molecule should be updated, according to this criterion.
needUpdate(IAtom) - Method in interface etomica.nbr.NeighborCriterion: Indicates whether the neighbor list for the given atom should be updated, according to this criterion.
Neff - Variable in class etomica.dimer.IntegratorDimerRT
negate() - Method in class etomica.veos.bigdecimal.BigSurd: Compute the negative.
negate() - Method in class etomica.veos.bigdecimal.BigSurdVec: Compute the negative.
negate() - Method in class etomica.veos.bigdecimal.Rational: Compute the negative.
negate() - Method in class org.jmol.util.Quaternion
negativeChop - Variable in class etomica.data.AccumulatorAverageBlockless
negativeChop - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
negativeChop - Variable in class etomica.data.AccumulatorAverageFixed
negativeChop - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
negativeExchange - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
neighborAtoms - Variable in class etomica.normalmode.P1ConstraintNbr
neighborAtoms - Variable in class etomica.normalmode.P1ConstraintNbrHcp
neighborBonds(int) - Method in class etomica.modules.render.ParseObj
NeighborCellManager - Class in etomica.nbr.cell: Class that defines and manages construction and use of lattice of cells for cell-based neighbor listing.
NeighborCellManager(ISimulation, IBox, double, ISpace) - Constructor for class etomica.nbr.cell.NeighborCellManager: Constructs manager for neighbor cells in the given box.
NeighborCellManager(ISimulation, IBox, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.NeighborCellManager: Construct manager for neighbor cells in the given box.
NeighborCellManagerList - Class in etomica.nbr.list: Subclass of NeighborCellManager that notifies the NeighborListManager when an atom added to the box gets a cell.
NeighborCellManagerList(ISimulation, IBox, double, ISpace) - Constructor for class etomica.nbr.list.NeighborCellManagerList
NeighborCellManagerList(ISimulation, IBox, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.NeighborCellManagerList
NeighborCellManagerListMolecular - Class in etomica.nbr.list.molecule: Subclass of NeighborCellManager that notifies the NeighborListManager when an atom added to the box gets a cell.
NeighborCellManagerListMolecular(ISimulation, IBox, double, ISpace) - Constructor for class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
NeighborCellManagerListMolecular(ISimulation, IBox, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
NeighborCellManagerMolecular - Class in etomica.nbr.cell.molecule: Class that defines and manages construction and use of lattice of cells for cell-based neighbor listing.
NeighborCellManagerMolecular(ISimulation, IBox, double, ISpace) - Constructor for class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Constructs manager for neighbor cells in the given box.
NeighborCellManagerMolecular(ISimulation, IBox, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Construct manager for neighbor cells in the given box.
NeighborCellManagerThreaded - Class in etomica.threaded.domain
NeighborCellManagerThreaded(ISimulation, IBox, double, ISpace) - Constructor for class etomica.threaded.domain.NeighborCellManagerThreaded
NeighborCellManagerThreaded(ISimulation, IBox, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.threaded.domain.NeighborCellManagerThreaded
neighborCount - Variable in class etomica.lattice.RectangularLatticeNbrIterator
NeighborCriterion - Interface in etomica.nbr: Atom filter used to specify whether two atoms are considered neighbors, for the purpose of tabulating neighbor lists.
NeighborCriterionMolecular - Interface in etomica.nbr.molecule: Atom filter used to specify whether two atoms are considered neighbors, for the purpose of tabulating neighbor lists.
neighborIterator - Variable in class etomica.association.MCMoveDimer
neighborIterator - Variable in class etomica.association.MCMoveDimerRotate
neighborIterator - Variable in class etomica.association.MCMoveSmer
neighborIterator - Variable in class etomica.association.MCMoveSmerRotate
neighborIterator - Variable in class etomica.integrator.mcmove.MCMoveDimer
neighborIterator - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
NeighborIterator(int, double) - Constructor for class etomica.lattice.CellLattice.NeighborIterator
neighborIterator - Variable in class etomica.nbr.site.PotentialMasterSite
neighborListAgentManager - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
neighborListAgentManager - Variable in class etomica.nbr.list.PotentialMasterList
neighborListAgentSource - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
neighborListAgentSource - Variable in class etomica.nbr.list.PotentialMasterList
NeighborListAgentSource(double, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
NeighborListAgentSourceColloid(double, ISpace) - Constructor for class etomica.modules.colloid.NeighborListManagerColloid.NeighborListAgentSourceColloid
NeighborListAgentSourceMolecular(double, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
NeighborListAgentSourceThreaded(double, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded.NeighborListAgentSourceThreaded
NeighborListEventManager - Class in etomica.nbr.list
NeighborListEventManager() - Constructor for class etomica.nbr.list.NeighborListEventManager
NeighborListEventManagerMolecular - Class in etomica.nbr.list.molecule
NeighborListEventManagerMolecular() - Constructor for class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
NeighborListManager - Class in etomica.nbr.list: Initiates the process of updating the neighbor lists.
NeighborListManager(PotentialMasterList, double, IBox, ISpace) - Constructor for class etomica.nbr.list.NeighborListManager: Configures instance for use by the given PotentialMaster.
NeighborListManager.AtomPotential1ListSource - Class in etomica.nbr.list
NeighborListManagerColloid - Class in etomica.modules.colloid
NeighborListManagerColloid(PotentialMasterList, double, IBox, ISpace) - Constructor for class etomica.modules.colloid.NeighborListManagerColloid
NeighborListManagerColloid.NeighborListAgentSourceColloid - Class in etomica.modules.colloid
NeighborListManagerMolecular - Class in etomica.nbr.list.molecule: Initiates the process of updating the neighbor lists.
NeighborListManagerMolecular(PotentialMasterListMolecular, double, IBox, ISpace) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerMolecular: Configures instance for use by the given PotentialMaster.
NeighborListManagerMolecular.MoleculePotential1ListSource - Class in etomica.nbr.list.molecule
NeighborListManagerSlanty - Class in etomica.nbr.list: Implements neighbor listing for a slanty box.
NeighborListManagerSlanty(PotentialMasterList, double, IBox, ISpace) - Constructor for class etomica.nbr.list.NeighborListManagerSlanty: Configures instance for use by the given PotentialMaster.
NeighborListManagerSlanty.NeighborListSlantyAgentSource - Class in etomica.nbr.list: Constructs instances of NeighborListManagerSlanty on behalf of the PotentialMaster
NeighborListManagerSlantyMolecular - Class in etomica.nbr.list.molecule: Implements neighbor listing for a slanty box.
NeighborListManagerSlantyMolecular(PotentialMasterListMolecular, double, IBox, ISpace) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular: Configures instance for use by the given PotentialMaster.
NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular - Class in etomica.nbr.list.molecule: Constructs instances of NeighborListManagerSlanty on behalf of the PotentialMaster
NeighborListManagerThreaded - Class in etomica.threaded.domain
NeighborListManagerThreaded(PotentialMasterListThreaded, double, IBox, ISpace) - Constructor for class etomica.threaded.domain.NeighborListManagerThreaded
neighborListNeighborsUpdated() - Method in class etomica.integrator.IntegratorHard
neighborListNeighborsUpdated() - Method in interface etomica.nbr.list.INeighborListListener
neighborListNeighborsUpdated() - Method in interface etomica.nbr.list.molecule.INeighborListListenerMolecular
neighborLists - Variable in class etomica.threaded.atom.PotentialMasterListWorker
neighborLists - Variable in class etomica.threaded.domain.PotentialMasterListWorker
NeighborListSlantyAgentSource(double, ISpace) - Constructor for class etomica.nbr.list.NeighborListManagerSlanty.NeighborListSlantyAgentSource
NeighborListSlantyAgentSourceMolecular(double, ISpace) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular
neighborManager - Variable in class etomica.graphics.ColorSchemeOverlap
neighborManager - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
neighborManager - Variable in class etomica.modules.mu.P1MagicWall
neighborManager - Variable in class etomica.normalmode.MeterMaxExpansion
neighborManager - Variable in class etomica.threaded.atom.PotentialMasterListWorker
neighborManager - Variable in class etomica.threaded.domain.PotentialMasterListWorker
neighborRadius2 - Variable in class etomica.nbr.CriterionSimple
neighborRadius2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
neighborRadiusSq - Variable in class etomica.normalmode.P1ConstraintNbr
neighborRadiusSq - Variable in class etomica.normalmode.P1ConstraintNbrHcp
neighbors - Variable in class etomica.lattice.RectangularLatticeNbrIterator
neighbors(int) - Method in class etomica.modules.render.ParseObj
neighborSetup() - Method in class etomica.modules.colloid.NeighborListManagerColloid
neighborSetup() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Reassigns all interacting atoms to cells, then loops over all cell-list neighbor pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list.
neighborSetup() - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular: Reassigns all interacting atoms to cells, then loops over all atom pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list.
neighborSetup() - Method in class etomica.nbr.list.NeighborListManager: Reassigns all interacting atoms to cells, then loops over all cell-list neighbor pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list.
neighborSetup() - Method in class etomica.nbr.list.NeighborListManagerSlanty: Reassigns all interacting atoms to cells, then loops over all atom pairs, determines for each pair whether a potential applies to it, and if so, puts each in the other's neighbor list.
neighborSetup() - Method in class etomica.threaded.domain.NeighborListManagerThreaded
NeighborSiteManager - Class in etomica.nbr.site: Neighbor manager for system in which there is an unchanging, one-to-one correspondence between atoms and lattice cells.
NeighborSiteManager(IBox, int, ISpace) - Constructor for class etomica.nbr.site.NeighborSiteManager: Constructs manager for neighbor cells in the given box.
neighborsUpdated() - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
neighborsUpdated() - Method in class etomica.nbr.list.NeighborListEventManager
nEthane - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
nEthane - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
new3(float, float, float) - Static method in class org.jmol.util.Point3f
new3(int, int, int) - Static method in class org.jmol.util.Point3i
new3(float, float, float) - Static method in class org.jmol.util.Vector3f
new4(float, float, float, float) - Static method in class org.jmol.util.AxisAngle4f: Constructs and initializes an AxisAngle4f from the specified x, y, z, and angle.
new4(float, float, float, float) - Static method in class org.jmol.util.Point4f
new4(float, float, float, float) - Static method in class org.jmol.util.Quaternion
newA(float[]) - Static method in class org.jmol.util.Matrix3f: Constructs and initializes a Matrix3f from the specified 9 element array.
newA(float[]) - Static method in class org.jmol.util.Matrix4f: Constructs and initializes a Matrix4f from the specified 16 element array.
newAA(AxisAngle4f) - Static method in class org.jmol.util.AxisAngle4f: Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
newAA(AxisAngle4f) - Static method in class org.jmol.util.Quaternion
newAndSetBit(int) - Static method in class org.jmol.util.BitSetUtil
newAntialiasing - Variable in class org.jmol.util.GData
newBitSet(int) - Static method in class org.jmol.util.BitSetUtil
newBitSet2(int, int) - Static method in class org.jmol.util.BitSetUtil
newBufferedImage(Object, int, int) - Method in interface org.jmol.api.ApiPlatform
newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
newByte2(int) - Static method in class org.jmol.util.ArrayUtil
newColor0 - Variable in class etomica.graph.operations.SplitOne.SplitOneParameters
newColor0() - Method in class etomica.graph.operations.SplitParameters
newColor1 - Variable in class etomica.graph.operations.SplitOne.SplitOneParameters
newColor1() - Method in class etomica.graph.operations.SplitParameters
newData - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
newFloat2(int) - Static method in class org.jmol.util.ArrayUtil
newFloat3(int, int) - Static method in class org.jmol.util.ArrayUtil
newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.ApiPlatform
newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
newGeo - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
newI(int) - Static method in class org.jmol.util.Rgb16
newInt2(int) - Static method in class org.jmol.util.ArrayUtil
newInt4(int) - Static method in class org.jmol.util.ArrayUtil
newLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
newLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
newM(double[][]) - Static method in class org.jmol.util.Eigen
newM(Matrix3f) - Static method in class org.jmol.util.Matrix3f: Constructs a new matrix with the same values as the Matrix3f parameter.
newM(Matrix4f) - Static method in class org.jmol.util.Matrix4f: Constructs a new matrix with the same values as the Matrix4f parameter.
newM(Matrix3f) - Static method in class org.jmol.util.Quaternion
newMesh(boolean, Tuple3f[], int, int[][], Tuple3f[], int) - Static method in class org.jmol.util.MeshSurface
newMV(Matrix3f, Vector3f) - Static method in class org.jmol.util.Matrix4f: Constructs and initializes a Matrix4f from the rotation matrix and translation.
newN(int) - Static method in class org.jmol.util.BitSet: Creates a bit set whose initial size is large enough to explicitly represent bits with indices in the range 0 through nbits-1.
newN(int) - Static method in class org.jmol.util.StringXBuilder
newOffScreenImage(int, int) - Method in interface org.jmol.api.ApiPlatform
newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
newOriginB - Variable in class etomica.action.IntegratorDimerApproach
newP(Tuple3f) - Static method in class org.jmol.util.Point3f
newP4(Point4f) - Static method in class org.jmol.util.Quaternion
newPartners - Variable in class etomica.potential.PotentialReactive.BondChangeData
newPosition - Variable in class etomica.dimer.IntegratorDimerRT
newPositionC - Variable in class etomica.association.BiasVolume2SiteAceticAcid
newPositionC - Variable in class etomica.association.BiasVolumeAceticAcid
newPt(Point4f) - Static method in class org.jmol.util.Point4f
newQ(Quaternion) - Static method in class org.jmol.util.Quaternion
newR - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
newS(String) - Static method in class org.jmol.util.StringXBuilder
newScriptVariableBs(BitSet, int) - Static method in class org.jmol.script.ScriptVariable
newScriptVariableIntValue(int, int, Object) - Static method in class org.jmol.script.ScriptVariable
newScriptVariableToken(Token) - Static method in class org.jmol.script.ScriptVariable
newSeeds - Variable in class etomica.virial.simulations.SimulationVirial
newShort2(int) - Static method in class org.jmol.util.ArrayUtil
newSlab(Point3f[], int, float[], int[][], int, int) - Static method in class org.jmol.util.MeshSurface
newSmerList - Variable in class etomica.association.MCMoveSmer
newSmerList - Variable in class etomica.association.MCMoveSmerRotate
newToken(int, int) - Static method in class org.jmol.script.Token
newTokenIntVal(int, int, Object) - Static method in class org.jmol.script.Token
newTokenObj(int, Object) - Static method in class org.jmol.script.Token
Newton - Class in etomica.units: The Newton unit of force, equal to 1 kg-m/s^2.
NewtonMinimization - Class in etomica.util.numerical
NewtonMinimization(FunctionMultiDimensionalDifferentiable, boolean) - Constructor for class etomica.util.numerical.NewtonMinimization
newtonRaphson(double, int, double, double, P1IntraMolecular) - Static method in class etomica.virial.simulations.VirialH2PIXC
newTotalCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
newU - Variable in class etomica.models.nitrogen.MeterDirectInitPert
newU - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
newU - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
newV(Tuple3f) - Static method in class org.jmol.util.Vector3f
newVA(Vector3f, float) - Static method in class org.jmol.util.AxisAngle4f: Constructs and initializes an AxisAngle4f from the specified axis and angle.
newVA(Tuple3f, float) - Static method in class org.jmol.util.Quaternion
newVariable(int, Object) - Static method in class org.jmol.script.ScriptVariable
newVertexBitSet() - Static method in class org.jmol.util.Normix
newWindowHeight - Variable in class org.jmol.util.GData
newWindowWidth - Variable in class org.jmol.util.GData
nex - Static variable in class etomica.potential.P2HydrogenPatkowski
nex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
NexpStretchFit - Static variable in class etomica.statmech.HardSphereFluid
NexpVirial - Static variable in class etomica.statmech.HardSphereFluid
next() - Method in class etomica.atom.AtomLeafAgentManager.AgentIterator
next() - Method in class etomica.atom.AtomTypeAgentManager.AgentIterator
next() - Method in class etomica.atom.iterator.ANIntergroupCoupled
next() - Method in class etomica.atom.iterator.ANIntergroupExchange
next() - Method in class etomica.atom.iterator.ANIntragroupExchange
next() - Method in class etomica.atom.iterator.ApiIndexList: Returns the iterator's pair and unsets iterator.
next() - Method in class etomica.atom.iterator.ApiInnerVariable: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.ApiInterArrayList: Returns the next iterate pair.
next() - Method in class etomica.atom.iterator.ApiIntergroup: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.ApiIntergroupCoupled: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.ApiIntergroupExchange: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.ApiIntergroupIntraSpecies: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.ApiIntraArrayList: Returns the next iterate pair.
next() - Method in class etomica.atom.iterator.ApiIntragroup
next() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
next() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Same as nextAtom.
next() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Same as nextAtom().
next() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
next() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
next() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
next() - Method in class etomica.atom.iterator.AtomIteratorNull
next() - Method in class etomica.atom.iterator.AtomIteratorSinglet
next() - Method in interface etomica.atom.iterator.AtomLeafsetIterator: Returns the next AtomSet iterate, or null if hasNext() is false.
next() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList: Same as nextSet().
next() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
next() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
next - Variable in class etomica.atom.iterator.MoleculeIteratorAll
next() - Method in class etomica.atom.iterator.MoleculeIteratorAll
next() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Same as nextAtom().
next() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet
next() - Method in interface etomica.atom.iterator.MoleculesetIterator: Returns the next AtomSet iterate, or null if hasNext() is false.
next() - Method in class etomica.atom.iterator.MpiInnerFixed: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.MpiInnerVariable: Returns the next pair of atoms.
next() - Method in class etomica.atom.iterator.MpiInterArrayList: Returns the next iterate pair.
next() - Method in class etomica.atom.iterator.MpiInterspecies1A
next() - Method in class etomica.atom.iterator.MpiInterspeciesAA: Returns the next iterate pair.
next() - Method in class etomica.atom.iterator.MpiIntraArrayList: Returns the next iterate pair.
next() - Method in class etomica.atom.iterator.MpiIntraspecies1A
next() - Method in class etomica.atom.iterator.MpiIntraspeciesAA: Returns the next iterate pair.
next() - Method in class etomica.atom.iterator.MpiMolecule: Same as nextPair.
next - Variable in class etomica.atom.iterator.TripletInnerSequential
next() - Method in class etomica.atom.iterator.TripletInnerSequential
next() - Method in class etomica.atom.MoleculeAgentManager.AgentIterator
next() - Method in class etomica.atom.SpeciesAgentManager.AgentIterator
next() - Method in class etomica.box.BoxAgentManager.AgentIterator
next() - Method in class etomica.graph.iterators.CartesianIterator
next() - Method in class etomica.graph.iterators.CartesianPermutator
next() - Method in class etomica.graph.iterators.ChainedIterator
next() - Method in class etomica.graph.iterators.DefaultIterator
next() - Method in class etomica.graph.iterators.DefaultPermutator
next() - Method in class etomica.graph.iterators.EdgelessIterator
next() - Method in class etomica.graph.iterators.filters.GlobalFilter
next() - Method in class etomica.graph.iterators.filters.LocalFilter
next() - Method in class etomica.graph.iterators.FixedEdgeCountIterator
next() - Method in class etomica.graph.iterators.IteratorWrapper
next() - Method in class etomica.graph.iterators.RangePermutator
next() - Method in class etomica.graph.iterators.StoredIterator
next() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
next() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
next() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
next() - Method in interface etomica.lattice.IndexIterator
next - Variable in class etomica.lattice.IndexIteratorIncreasing
next() - Method in class etomica.lattice.IndexIteratorIncreasing: Returns the next index.
next() - Method in class etomica.lattice.IndexIteratorRectangular: Returns the next iterate, or null if hasNext is false.
next() - Method in class etomica.lattice.IndexIteratorReflecting
next() - Method in class etomica.lattice.IndexIteratorTriangular: Returns the next iterate.
next() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
next() - Method in class etomica.lattice.RectangularLattice.Iterator
next() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Returns the next site in the iteration sequence, or null if hasNext is false.
next() - Method in interface etomica.lattice.SiteIterator: Returns the next iterate.
next() - Method in class etomica.math.discrete.CombinationIterator
next() - Method in class etomica.math.discrete.FixedSumIterator: Returns the next iterate, or null if iterator has expired.
next() - Method in class etomica.math.discrete.PermutationDegenerateIterator: Returns the next iterate, or null if hasNext is false.
next() - Method in class etomica.math.discrete.PermutationIterator
next() - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder
next() - Method in class etomica.nbr.cell.Api1ACell
next() - Method in class etomica.nbr.cell.AtomIteratorCell
next() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
next() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
next() - Method in class etomica.nbr.site.Api1ASite
next - Variable in class etomica.potential.PotentialGroup.PotentialLinker
next() - Method in class etomica.potential.PotentialMaster.AtomIterator0
next() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
next - Variable in class etomica.util.EventManager.Linker
next - Variable in class etomica.util.FunctionChain.Link
next(int) - Method in class etomica.util.MersenneTwister: Returns an integer with bits bits filled with a random number.
next() - Method in class etomica.virial.cluster.PermutationIterator
next() - Method in class etomica.virial.PYGenerator.IteratorEF
next() - Method in interface g3dsys.control.IndexIterator: Get the next set of indices
next - Static variable in class org.jmol.script.Token
nextAtom - Variable in class etomica.association.MCMoveVolumeAssociated.Agent
nextAtom() - Method in interface etomica.atom.iterator.AtomIterator: Returns the next atom in the iteration sequence, or null if hasNext() is false.
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorArrayList: Returns the next iterate and advances the iterator.
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Returns the next iterator, or null if hasNext is false.
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Returns the next iterate and advances the iterator.
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorNull
nextAtom() - Method in class etomica.atom.iterator.AtomIteratorSinglet: Returns the iterator's atom and unsets iterator.
nextAtom() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
nextAtom() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
nextAtom() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
nextAtom() - Method in class etomica.nbr.cell.AtomIteratorCell
nextBoolean() - Method in class etomica.util.MersenneTwister: This method is missing from jdk 1.0.x and below.
nextBoolean() - Method in class etomica.util.MersenneTwisterFast
nextByte() - Method in class etomica.util.MersenneTwister: For completeness' sake, though it's not in java.util.Random.
nextByte() - Method in class etomica.util.MersenneTwisterFast
nextBytes(byte[]) - Method in class etomica.util.MersenneTwister: A bug fix for all versions of the JDK.
nextBytes(byte[]) - Method in class etomica.util.MersenneTwisterFast
nextChar() - Method in class etomica.util.MersenneTwister: For completeness' sake, though it's not in java.util.Random.
nextChar() - Method in class etomica.util.MersenneTwisterFast
nextClearBit(int) - Method in class org.jmol.util.BitSet: Returns the index of the first bit that is set to false that occurs on or after the specified starting index.
nextCriterion() - Method in class etomica.atom.iterator.IteratorDirective.PotentialCriterion
nextCursor - Variable in class etomica.atom.iterator.MoleculeIteratorAll
nextDouble() - Method in interface etomica.api.IRandom: Returns a pseudorandom double, uniformly distributed between 0.0 (exclusive) and 1.0 (exclusive).
nextDouble() - Method in class etomica.util.MersenneTwister: A bug fix for versions of JDK 1.1 and below.
nextDouble() - Method in class etomica.util.MersenneTwisterFast
nextDouble() - Method in class etomica.util.RandomMersenneTwister
nextDouble() - Method in class etomica.util.RandomNumberGenerator
nextDouble() - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a random double, uniformly distributed between 0 and 1.
nextFixedDouble() - Method in interface etomica.api.IRandom: Returns a pseudorandom double, uniformly distributed between 0.0 (inclusive) and 1.0 (exclusive).
nextFixedDouble() - Method in class etomica.util.RandomMersenneTwister
nextFixedDouble() - Method in class etomica.util.RandomNumberGenerator
nextFixedDouble() - Method in class etomica.util.RandomNumberGeneratorUnix
nextFloat() - Method in class etomica.util.MersenneTwister: A bug fix for versions of JDK 1.1 and below.
nextFloat() - Method in class etomica.util.MersenneTwisterFast
nextFloat() - Method in class etomica.util.RandomMersenneTwister
nextFloat() - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a random float, uniformly distributed between 0 and 1.
nextGaussian() - Method in interface etomica.api.IRandom: Returns a pseudorandom double, Gaussian ("normally") distributed value with mean 0.0 and standard deviation 1.0.
nextGaussian() - Method in class etomica.util.MersenneTwisterFast
nextGaussian - Variable in class etomica.util.RandomMersenneTwister
nextGaussian() - Method in class etomica.util.RandomMersenneTwister
nextGaussian() - Method in class etomica.util.RandomNumberGenerator
nextGaussian - Variable in class etomica.util.RandomNumberGeneratorUnix
nextGaussian() - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a double taken from a Gaussian distribution with 0 mean and variance of 1.
nextIndex() - Method in class etomica.lattice.RectangularLattice.Iterator
nextIndex() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Returns the index of the next iterate while advancing the iterator.
nextIndex() - Method in interface etomica.lattice.SiteIterator: Returns the index of the next iterate while advancing iterator.
nextInt(int) - Method in interface etomica.api.IRandom: Returns a pseudorandom integer, uniformly distributed between 0 (inclusive) and maxInt (exclusive).
nextInt(int) - Method in class etomica.util.MersenneTwister: This method is missing from JDK 1.1 and below.
nextInt() - Method in class etomica.util.MersenneTwisterFast
nextInt(int) - Method in class etomica.util.MersenneTwisterFast: Returns an integer drawn uniformly from 0 to n-1.
nextInt() - Method in class etomica.util.RandomMersenneTwister
nextInt(int) - Method in class etomica.util.RandomMersenneTwister: Returns a random int ranging from 0 to max-1.
nextInt(int) - Method in class etomica.util.RandomNumberGenerator
nextInt() - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a random int (32-bit integer).
nextInt(int) - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a random int ranging from 0 to max-1.
nextLeft - Variable in class etomica.util.TreeLinker
nextLong() - Method in class etomica.util.MersenneTwisterFast
nextLong() - Method in class etomica.util.RandomMersenneTwister
nextLong() - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a random long (64-bit integer).
nextLong(long) - Method in class etomica.util.RandomNumberGeneratorUnix: Returns a random long ranging from 0 to max-1.
nextMolecule - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule.Agent
nextMolecule() - Method in interface etomica.atom.iterator.MoleculeIterator: Returns the next atom in the iteration sequence, or null if hasNext() is false.
nextMolecule() - Method in class etomica.atom.iterator.MoleculeIteratorArrayList: Returns the next iterate and advances the iterator.
nextMolecule() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Returns the next iterate and advances the iterator.
nextMolecule() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet: Returns the iterator's atom and unsets iterator.
nextMolecule() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
nextOp - Variable in class etomica.graph.operations.UnaryChain
nextPair(NodePair) - Method in interface etomica.graph.isomorphism.SearchState
nextPair(NodePair) - Method in class etomica.graph.isomorphism.UllmanSearchState
nextPair(NodePair) - Method in class etomica.graph.isomorphism.VF2SearchState
nextPair(NodePair) - Method in class etomica.graph.isomorphism.VFSearchState
nextPair() - Method in class etomica.nbr.cell.ApiAACell
nextPair() - Method in class etomica.nbr.cell.molecule.MpiAACell
nextParams - Variable in class etomica.graph.operations.UnaryChain.ChainParameters
nextprime(BigInteger) - Method in class etomica.veos.bigdecimal.Prime: return the smallest prime larger than n
nextRandom8Bit() - Static method in class org.jmol.util.Shader: Implements RANDU algorithm for random noise in lighting/shading.
nextReweightStep - Variable in class etomica.virial.MeterVirialBDBin
nextReweightStep - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
nextReweightStep - Variable in class etomica.virial.MeterVirialBinMultiThreaded
nextReweightStep - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
nextRight - Variable in class etomica.util.TreeLinker
nextSet() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList: Returns the iterator's pair and unsets iterator.
nextSetBit(int) - Method in class org.jmol.util.BitSet: Returns the index of the first bit that is set to true that occurs on or after the specified starting index.
nextShort() - Method in class etomica.util.MersenneTwister: For completeness' sake, though it's not in java.util.Random.
nextShort() - Method in class etomica.util.MersenneTwisterFast
nextVector() - Method in class etomica.config.ConformationChain
nextVector() - Method in class etomica.config.ConformationChain2D
nextVector() - Method in class etomica.config.ConformationChain3D
nextVector() - Method in class etomica.config.ConformationChainZigZag
nextVector() - Method in class etomica.config.ConformationChainZigZag2
nf - Variable in class etomica.virial.ClusterChainSoft
nf - Variable in class etomica.virial.ClusterSinglyConnected
nf - Variable in class etomica.virial.ClusterWheatleyExtendSW
nf - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
nf1 - Variable in class etomica.virial.ClusterChainHS
nfBond - Variable in class etomica.virial.PYGenerator.IteratorEF
nfctmx - Static variable in class etomica.potential.P2O2Bartolomei
nFe - Variable in class etomica.meam.PotentialFeEAM_LS
nFieldPoints - Variable in class etomica.graph.operations.Mul.MulParameters
nGraft - Variable in class etomica.modules.colloid.ColloidGraphic.GraftAction
nGraft - Variable in class etomica.modules.colloid.ColloidSim
nGraft - Variable in class etomica.modules.colloid.ConfigurationColloid
Ni - Static variable in class etomica.meam.ParameterSetMEAM
nIn - Static variable in class org.jmol.util.Shader
nIndices - Variable in class etomica.virial.cluster.PermutationIterator
nInner - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
nInsert - Variable in class etomica.models.oneDHardRods.MeterWidomMode
nInsert - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
nInsert - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
nIntegrators - Variable in class etomica.integrator.IntegratorManagerMC
Nitrogen - Class in etomica.chem.elements: Class for the Nitrogen element.
Nitrogen(String) - Constructor for class etomica.chem.elements.Nitrogen
Nitrogen(String, double) - Constructor for class etomica.chem.elements.Nitrogen
nKs - Variable in class etomica.potential.EwaldSummation
nLayer - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
nLayer - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
nLayer - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
nLayer - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
nLayer - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
nLayer - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
nLayer - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
nLayer - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
nLayer - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
nLeafAtoms - Variable in class etomica.atom.iterator.ANIntergroupCoupled
nLeafAtoms - Variable in class etomica.atom.iterator.ANIntergroupExchange
nlin - Static variable in class etomica.models.water.P2WaterSzalewicz
nlin3 - Variable in class etomica.models.water.P2WaterSzalewicz
nLookUp - Static variable in class etomica.space3d.Vector3D
nLREP - Variable in class etomica.meam.PotentialCuLREP
nm - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
nm - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
nm - Variable in class etomica.normalmode.HessianDB
nm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
nm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
nm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
nMax - Static variable in class etomica.veos.bigdecimal.PartitionsP: The maximum integer covered by the high end of the list.
nMax - Static variable in class etomica.veos.bigdecimal.Prime: The maximum integer covered by the high end of the list.
nMethane - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
nMethane - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
NModifier() - Constructor for class etomica.modules.crystalviewer.LatticeEditor.NModifier
nMol - Variable in class etomica.normalmode.MeterSolidProps
nMol - Variable in class etomica.normalmode.MeterSolidPropsLJ
nMol - Variable in class etomica.normalmode.PotentialCalculationEFSSP
nMol - Variable in class etomica.normalmode.PotentialCalculationLJSP
nMolecules - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule.Agent
nMolecules - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
nMolecules - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
nMolecules - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
nMoments - Variable in class etomica.data.AccumulatorAverageCollapsingLog
nMonoAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
nMonoOl - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
nmrurlformat - Static variable in class org.jmol.script.Token
nMu - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
nMu - Variable in class etomica.normalmode.DataSourcePMu
nNominalAtoms - Variable in class etomica.modules.droplet.DropletAtomic
nO2 - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
NO_MORE_ACTIONS - Static variable in class etomica.action.activity.ControllerEvent
nocontourlines - Static variable in class org.jmol.script.Token
Node - Interface in etomica.graph.model
node1ID - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
node2ID - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
NODE_NULL - Static variable in interface etomica.graph.traversal.Traversal
nodeColor - Variable in class etomica.virial.cluster.VirialDiagrams
nodeColor - Variable in class etomica.virial.cluster.VirialDiagramsMix
nodeColor - Variable in class etomica.virial.cluster.VirialDiagramsPT
nodeColors - Variable in class etomica.virial.cluster.VirialDiagramsMix
nodeColors - Variable in class etomica.virial.cluster.VirialDiagramsMix2
nodeCount() - Method in interface etomica.graph.model.Graph
nodeCount() - Method in class etomica.graph.model.impl.GraphImpl
nodeId() - Method in class etomica.graph.operations.ConvParameters
nodeId - Variable in class etomica.graph.operations.FactorOnce.FactorOnceParameters
nodeId() - Method in class etomica.graph.operations.IntParameters
NodeImpl - Class in etomica.graph.model.impl
NodeImpl(byte, char, char) - Constructor for class etomica.graph.model.impl.NodeImpl
NodePair - Class in etomica.graph.isomorphism
NodePair(Byte, Byte) - Constructor for class etomica.graph.isomorphism.NodePair
nodes() - Method in interface etomica.graph.model.Graph
nodes() - Method in class etomica.graph.model.impl.GraphImpl
nodesToString() - Method in interface etomica.graph.model.Graph
nodesToString() - Method in class etomica.graph.model.impl.GraphImpl
NodeVisitor - Interface in etomica.graph.model
NoDoNotRemoveSpeciesButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
nodots - Static variable in class org.jmol.script.Token
nofill - Static variable in class org.jmol.script.Token
noisyAdjustment - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
nomesh - Static variable in class org.jmol.script.Token
nominalBlockSize - Variable in class etomica.data.AccumulatorAverageCollapsing
nominalBondL - Static variable in class etomica.virial.SpeciesAlkane
nominalBondL - Static variable in class etomica.virial.SpeciesFactorySiepmannSpheres
nominalBondL - Static variable in class etomica.virial.SpeciesFactorySpheres2
nominalBondTheta - Static variable in class etomica.virial.SpeciesAlkane
nominalBondTheta - Static variable in class etomica.virial.SpeciesFactorySiepmannSpheres
nominalBondTheta - Static variable in class etomica.virial.SpeciesFactorySpheres2
nominalBoxSize - Variable in class etomica.normalmode.MCMoveVolumeSolid
nominalDeltaX - Variable in class etomica.util.HistogramCollapsing
nominalDiameter - Variable in class etomica.modules.droplet.EllipseDisplayAction
nominalFluctuation - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
nominalFrequency - Variable in class etomica.integrator.mcmove.MCMove: Value giving nominal frequency for performing this move.
nominalNumAtoms - Variable in class etomica.normalmode.DataSourcePN
nominalScale - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
nominalTheta - Variable in class etomica.normalmode.MeterThetaDeviation
nominalTimeStep - Variable in class etomica.graphics.DeviceDelaySlider
nominalWeight - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
nominalWeight - Variable in class etomica.virial.MeterVirialBinMultiThreaded
nominalWeight - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
nonAdditive - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
nonAdditive - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
nonAdditive - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
nonAdditive - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
nonAdditive - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
nonAdditive - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
nonAdditiveOnly - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
nonAssociationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
nonAssociationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
nonAssociationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
NONE - Static variable in class etomica.virial.cluster.ClusterOperations
none - Static variable in class org.jmol.script.Token
nonintervalAction(IntegratorNonintervalEvent) - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
NonintervalEventType(String) - Constructor for class etomica.integrator.IntegratorNonintervalEvent.NonintervalEventType
nonLinearCG(FunctionMultiDimensionalDifferentiable, double[]) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
NonLinearConjugateGradients - Class in etomica.conjugategradient
NonLinearConjugateGradients() - Constructor for class etomica.conjugategradient.NonLinearConjugateGradients
NonLinearCurveDiffFitting - Class in etomica.util.numerical: Similar as but fit the difference See for fundamental implementation details
NonLinearCurveDiffFitting(String, int, int) - Constructor for class etomica.util.numerical.NonLinearCurveDiffFitting
NonLinearCurveFitting - Class in etomica.util.numerical: Class that compute Reference: NUMERICAL RECIPES in Fortran 2nd Ed.
NonLinearCurveFitting(String, int, int) - Constructor for class etomica.util.numerical.NonLinearCurveFitting
NoOfSpheres - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
noOfSteps - Variable in class etomica.virial.GUI.models.ModelTemperatureAndSteps
noReset - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
norm - Variable in class etomica.math.Quaternion
norm - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
norm - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
norm0 - Variable in class etomica.potential.P2SpheroPolyhedron
norm1 - Variable in class etomica.potential.P2SpheroPolyhedron
norm2 - Variable in class etomica.potential.P2SpheroPolyhedron
normal - Variable in class etomica.dimer.SimDimerLJadatom
normal - Variable in class etomica.dimer.SimDimerMEAMadatom
normalCount - Variable in class org.jmol.util.MeshSurface
normalD - Variable in class etomica.dimer.IntegratorDimerMin
normalDir - Variable in class etomica.dimer.SimDimerLJadatom
normalize() - Method in interface etomica.api.IVectorMutable: Normalizes this vector, so this.squared() == 1.
normalize() - Method in class etomica.math.Quaternion: Normalizes the Quaternion q i.e.
normalize() - Method in class etomica.space1d.Vector1D
normalize() - Method in class etomica.space2d.Vector2D
normalize() - Method in class etomica.space3d.Vector3D
normalize() - Method in class etomica.spaceNd.VectorND
normalize() - Method in class etomica.veos.bigdecimal.BigSurd: Normalize to squarefree discriminant.
normalize() - Method in class etomica.veos.bigdecimal.BigSurdVec: Combine terms that can be written as a single surd.
normalize() - Method in class etomica.veos.bigdecimal.Rational: Normalize to coprime numerator and denominator.
normalize() - Method in class org.jmol.util.Vector3f: Normalizes this vector in place.
normalizeG() - Method in class etomica.veos.bigdecimal.BigSurd: Normalize to coprime numerator and denominator in prefactor and discriminant
NormalModeAnalysisDisplay1D - Class in etomica.normalmode
NormalModeAnalysisDisplay1D(Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1D
NormalModeAnalysisDisplay1D.Applet - Class in etomica.normalmode
NormalModeAnalysisDisplay1DGraphic - Class in etomica.normalmode
NormalModeAnalysisDisplay1DGraphic(NormalModeAnalysisDisplay1D, Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
NormalModeAnalysisDisplay1DGraphic.Applet - Class in etomica.normalmode
NormalModeAnalysisDisplay2D - Class in etomica.normalmode: Harmonic anaylsis for 2-D soft-sphere model
NormalModeAnalysisDisplay2D(ISpace) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2D
NormalModeAnalysisDisplay2DGraphic - Class in etomica.normalmode
NormalModeAnalysisDisplay2DGraphic(NormalModeAnalysisDisplay2D, Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
NormalModeAnalysisDisplay2DGraphic.Applet - Class in etomica.normalmode
NormalModeAnalysisDisplay3D - Class in etomica.normalmode
NormalModeAnalysisDisplay3D(Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3D
NormalModeAnalysisDisplay3D.Applet - Class in etomica.normalmode
NormalModeAnalysisDisplay3DGraphic - Class in etomica.normalmode: Harmonic Oscillator 3D
NormalModeAnalysisDisplay3DGraphic(NormalModeAnalysisDisplay3D, Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
NormalModeAnalysisDisplay3DGraphic.Applet - Class in etomica.normalmode
NormalModeEigenGetter - Class in etomica.normalmode
NormalModeEigenGetter() - Constructor for class etomica.normalmode.NormalModeEigenGetter
NormalModeEigenGetter - Class in etomica.paracetamol
NormalModeEigenGetter() - Constructor for class etomica.paracetamol.NormalModeEigenGetter
normalModes - Variable in class etomica.models.hexane.SimHarmonicHexane
normalModes - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
normalModes - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
normalModes - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
normalModes - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
normalModes - Variable in class etomica.normalmode.MCMovePhaseAngle
normalModes - Variable in class etomica.normalmode.MCMoveWV
normalModes - Variable in class etomica.normalmode.MeterHarmonicEnergy
normalModes - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
normalModes - Variable in class etomica.normalmode.MeterJacobian
NormalModes - Interface in etomica.normalmode: Provides information about all the normal modes for a periodic system.
normalModes - Variable in class etomica.normalmode.SimBennet
normalModes - Variable in class etomica.normalmode.SimHarmonic
normalModes - Variable in class etomica.normalmode.SimHarmonicUmbrella
normalModes - Variable in class etomica.normalmode.SimModesJ
normalModes - Variable in class etomica.normalmode.SimOverlap
normalModes - Variable in class etomica.normalmode.SimOverlapLJ
normalModes - Variable in class etomica.normalmode.SimOverlapLJModule
normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphere
normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
normalModes - Variable in class etomica.normalmode.SimOverlapSSnxy
normalModes - Variable in class etomica.normalmode.SimTargetUmbrella
normalModes - Variable in class etomica.normalmode.SimUmbrella
normalModes - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
NormalModes1DHR - Class in etomica.normalmode: Normal-mode quantities for a 1-dimensional system of hard rods.
NormalModes1DHR(IBoundary, int) - Constructor for class etomica.normalmode.NormalModes1DHR
NormalModes2D - Class in etomica.normalmode
NormalModes2D(ISpace, IBoundary, Primitive, Basis) - Constructor for class etomica.normalmode.NormalModes2D
NormalModes3D - Class in etomica.normalmode
NormalModes3D(ISpace, Primitive, Basis) - Constructor for class etomica.normalmode.NormalModes3D
NormalModesFromFile - Class in etomica.normalmode: Provides normal-mode information as obtained from a file read at construction.
NormalModesFromFile(String, int) - Constructor for class etomica.normalmode.NormalModesFromFile
NormalModesMolecular - Class in etomica.normalmode: Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis, occupied by atoms that interact with a simple, spherically-symmetric soft potential.
NormalModesMolecular(SpeciesWater4P, boolean, IPotentialMaster, IBox, int[], Primitive, int, LatticeSumMolecularCrystal.AtomicTensorAtomicPair, ISpace) - Constructor for class etomica.normalmode.NormalModesMolecular
NormalModesPotential - Class in etomica.normalmode: Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis, occupied by atoms that interact with a simple, spherically-symmetric soft potential.
NormalModesPotential(int[], Primitive, Basis, Potential2SoftSpherical, ISpace) - Constructor for class etomica.normalmode.NormalModesPotential
NormalModesPotentialParacetamol - Class in etomica.paracetamol: Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis, occupied by atoms that interact with a simple, spherically-symmetric soft potential.
NormalModesPotentialParacetamol(int[], Primitive, Basis, ISpace) - Constructor for class etomica.paracetamol.NormalModesPotentialParacetamol
NormalModesPotentialParacetamol.Lattice2ndDerivative - Class in etomica.paracetamol
NormalModesSoftSpherical - Class in etomica.normalmode: Computes the normal modes for a Bravais lattice occupied by atoms that interact with a simple, spherically-symmetric soft potential, using analysis of second derivatives.
NormalModesSoftSpherical(int[], Primitive, Potential2SoftSpherical, ISpace) - Constructor for class etomica.normalmode.NormalModesSoftSpherical
NormalModesVariable - Class in etomica.normalmode
NormalModesVariable(ISpace, int, CoordinateDefinition) - Constructor for class etomica.normalmode.NormalModesVariable
normals - Variable in class org.jmol.util.MeshSurface
normalsTemp - Variable in class org.jmol.util.MeshSurface
normalVector - Variable in class etomica.virial.MCMoveClusterAtomHSRing
normalWidth - Variable in class etomica.virial.MCMoveClusterAtomHSRing
Normix - Class in org.jmol.util: Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Normix() - Constructor for class org.jmol.util.Normix
NORMIX_NULL - Static variable in class org.jmol.util.Normix
normixCount - Variable in class org.jmol.util.MeshSurface
noRotScale - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
NORTH - Static variable in class etomica.util.Constants.CompassDirection
not() - Method in interface etomica.graph.model.Bitmap: Inverts the bits of this bitmap: bitmap = ~bitmap.
not() - Method in class etomica.graph.model.impl.AbstractBitmap
not() - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1).
not() - Method in class etomica.graph.model.impl.BitmapOfLongVector
NOT_ALLOWED - Static variable in class etomica.units.Prefix: Constant used when invoking constructor of SimpleUnit class to indicate that the unit does not permit the use of a prefix.
NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JmolConstants
notfrontonly - Static variable in class org.jmol.script.Token
notifyEndOfRendering() - Method in interface org.jmol.api.ApiPlatform
notifyEndOfRendering() - Method in class org.jmol.awt.Platform
notifyEnergyChange(double) - Method in class etomica.integrator.IntegratorMC
notifyNeedUpdate() - Method in class etomica.graphics.EtomicaPlot: Notify that the displayPlot has new data, but we're not showing.
notifyNewMolecules(ISpecies, int, int) - Method in class etomica.box.Box: Notifies the SpeciesMaster that the given number of new Atoms will be added to the system.
notriangles - Static variable in class org.jmol.script.Token
notzero - Variable in class etomica.virial.ClusterWheatleyHS
notzero - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
nOut - Static variable in class org.jmol.util.Shader
nOuter - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
NoValueOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
nOverlaps - Variable in class etomica.graphics.ColorSchemeOverlap
nOverlaps - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
nPairs() - Method in class etomica.potential.Potential0Lrc: Returns the number of pairs formed from molecules of the current species, in the given box.
npairs - Variable in class etomica.virial.ClusterWheatleyExtendSW
npairs - Variable in class etomica.virial.MeterVirialSWWE
nPerm - Variable in class etomica.potential.P3HydrogenManzhos
nPermutations - Variable in class etomica.virial.ClusterBonds
nPermutations() - Method in class etomica.virial.ClusterBonds: Number of permutations of (and including) the basic cluster used when calculating its value for a configuration
nPoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
nPoints - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
nPoints - Variable in class etomica.virial.ClusterBonds
nPoints - Variable in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
nPoints - Variable in class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
nPoints - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
nPoints - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
nPoints - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
nPoints - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
nPoints - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
nPoints - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
nPoints - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
nPoints - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
nPoints - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
nPoints - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
nPoints - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
nPoints - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
nPoints - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
nPoints - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
nPoints - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
nPoints - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
nPoints - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
nPoints - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
nPoints - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
nPoints - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
nPoints - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
nPoints - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
nPoints - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
nPoints - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
nPoints - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
nPoints - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
nPoints - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
nPoints - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
nPoints - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
nPoints - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
nPoints - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
nPoints - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
nPoints - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
nPoints - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
nPoints - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
nPoints - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
nPoints - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
nPoints - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
nPoints - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
nPoints - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
nPoints - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
nPoints - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
nPoints - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
nPoints - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
nPoints - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
nPoints - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
nPoints - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
nPoints - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
nPoints - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
nPoints - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
nPoints - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
nPoints - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
nPoints - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
nPoints - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
nPoints - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
nPoints - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
nPoints - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
nPoints - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
npol - Static variable in class etomica.models.water.P2WaterSzalewicz
npowers - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nPretendPoints - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
nPts - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
nPtsTabulated - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
nPtsTabulated - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
nPtsTabulated - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
nPtsTabulated - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
npun - Static variable in class etomica.potential.P2O2Bartolomei
nRawData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
nRawDataDoubles - Variable in class etomica.data.AccumulatorAverageCollapsingLog
nrcMax - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
nrcMax - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
nReactCO - Variable in class etomica.modules.catalysis.ReactionManagerCO
nReacted - Variable in class etomica.modules.chainequilibrium.MeterConversion
nRealPoints - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
nRealShells - Variable in class etomica.potential.EwaldSummation
nRejected - Variable in class etomica.integrator.IntegratorMD
nRootField - Variable in class etomica.modules.clustergenerator.MyApplet
nRows - Variable in class etomica.data.types.DataTable.DataInfoTable
nRows - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
nRowsA - Variable in class etomica.normalmode.MeterSolidPropsLJ
nSamples - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
nSamples - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
nSamples - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
nSamples - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
nSets - Variable in class org.jmol.util.MeshSurface
nShapes - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
nShells - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
nShells - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
nShells - Variable in class etomica.meam.PotentialFeEAM_LS
nShells - Variable in class etomica.potential.Potential2SoftSphericalLS
nsite3 - Static variable in class etomica.models.water.P2WaterSzalewicz
nsitea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nsiteb - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nsitemax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nsites - Static variable in class etomica.models.co2.P2CO2Hellmann
nSlider - Variable in class etomica.modules.droplet.DropletGraphic
nSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
nSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
nSlider - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor
nsp - Static variable in class etomica.potential.P2HydrogenPatkowski
nsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
nSpheres - Variable in class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
nSpheres - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
nSpheres - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
nSpheres - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
nSpheres - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
nSpheres - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
nSpheres - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
nSpheres - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
nSpheres - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
nSpheres - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
nSpheres - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
nSpheres - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
nSpheres - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
Nstar - Variable in class etomica.dimer.IntegratorDimerMin
Nstar - Variable in class etomica.dimer.IntegratorDimerRT
NstarDelta - Variable in class etomica.dimer.IntegratorDimerMin
NstarDelta - Variable in class etomica.dimer.IntegratorDimerRT
nStates - Variable in class etomica.tmmc.IntegratorTMMC
nSubPoints - Variable in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
nSubPoints - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
nSurfaceBonds - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
nSurfaceSites - Variable in class etomica.modules.catalysis.P2SquareWellBonding
nSurfaceSites - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
nSurfactantSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
nTag - Variable in class etomica.data.AccumulatorAverageCollapsingLog
nTag - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
nTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
nThreads - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
nThreads - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
nTimes - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
nTimes - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
nTimes - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
nTimes - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
ntpot - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nTrial - Variable in class etomica.util.numerical.AkimaSplineSmoother
nTrial - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
nTrial - Variable in class etomica.virial.MCMoveClusterRingRegrow
nTrial - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
nTrials - Variable in class etomica.integrator.mcmove.MCMoveTracker
nType - Variable in class etomica.models.nitrogen.SpeciesN2
nType - Variable in class etomica.models.nitrogen.SpeciesN2B
nType - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
nType - Variable in class etomica.paracetamol.SpeciesParacetamol
ntypemax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
nTypes - Variable in class etomica.virial.ClusterWheatleySoftBDMix
nTypes - Variable in class etomica.virial.ClusterWheatleySoftMix
nTypes - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
nTypes - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
nTypes - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
nTypes - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
nTypes - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
nTypes - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
nucleic - Static variable in class org.jmol.script.Token
nufac0 - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
Null - Class in etomica.units: Dimension specified dimensionless quantities which have no other interpretation (e.g., the quantity is not known to be an angle, or a fraction).
NULL - Static variable in class etomica.units.Prefix: Prefix indicating 10⁰ = 1.
NULL_NODE - Static variable in interface etomica.graph.isomorphism.SearchState
nullCollisionTime - Variable in class etomica.integrator.IntegratorHard.Agent
nullPair() - Static method in class etomica.graph.isomorphism.NodePair
nullPotential - Variable in class etomica.integrator.IntegratorHard.Agent
nullPotentialManager - Variable in class etomica.integrator.IntegratorHard
nullRegionMethod - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
nullRegionMethod - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
nullRegionMethod - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
num - Variable in class etomica.virial.ClusterICPYC
numActions - Variable in class etomica.action.activity.ActivityGroupParallel
numActions - Variable in class etomica.action.activity.ActivityGroupSeries
numAlpha - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
numAlpha - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
numAlpha - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
numAlpha - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
numAlpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
numAlpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
numAlpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
numAlpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
numAlpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
numAlpha - Variable in class etomica.normalmode.MeterOverlapSwitch
numAlpha - Variable in class etomica.normalmode.MeterTargetTP
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
numAlpha - Variable in class etomica.overlap.MeterOverlap
numAlpha - Variable in class etomica.virial.simulations.SimulationVirialOverlap
numAlpha - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
numAssociatedAtoms - Variable in class etomica.association.MCMoveVolumeAssociated
numAssociatedMolecules - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
numAtoms - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
numAtoms - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numAtoms - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numAtoms - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numAtoms - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
numAtoms - Variable in class etomica.chem.models.ModelChain
numAtoms - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
numAtoms - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
numAtoms - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
numAtoms - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
numAtoms - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
numAtoms - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
numAtoms - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
numAtoms - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
numAtoms - Variable in class etomica.mappedvirial.MappedU.LJMDParams
numAtoms - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
numAtoms - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
numatoms - Variable in class etomica.meam.EFSTungsten.Params
numAtoms - Variable in class etomica.metastable.LJmuVT.LJMCParams
numAtoms - Variable in class etomica.metastable.LJNPT.LJMCParams
numAtoms - Variable in class etomica.metastable.LJNVT.LJMCParams
numAtoms - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
numAtoms - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
numAtoms - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
numAtoms - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
numAtoms - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
numAtoms - Variable in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
numAtoms - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
numAtoms - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
numAtoms - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
numAtoms - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
numAtoms - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
numAtoms - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
numAtoms - Variable in class etomica.normalmode.SimLJVacancy.LJParams
numAtoms - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
numAtoms - Variable in class etomica.surfacetension.LJMC.LJMCParams
numAtoms - Variable in class etomica.tests.TestHSMD3D.SimParams
numAtoms - Variable in class etomica.tests.TestLJMC3D.SimParams
numAtoms - Variable in class etomica.tests.TestSWChain.SimParams
numAtoms - Variable in class etomica.virial.CoordinatePairLeafSet
numAtoms - Variable in class etomica.virial.CoordinatePairMoleculeSet
numAtoms - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numAtomsLattice - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
numAtomsMove - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
numBeads - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
numberFraction - Variable in class etomica.species.SpeciesSpheresHetero
numberMolecules - Variable in class etomica.AlkaneEH.CH4NVT.Param
numberMolecules - Variable in class etomica.AlkaneEH.DHS_NVT.Param
numberMolecules - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
numberMolecules(ISpecies, int) - Method in class etomica.box.BoxEventManager
numberMolecules - Variable in class etomica.dielectric.DHS_NVT.Param
numberMolecules - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
numberMolecules - Variable in class etomica.dielectric.TIP4P_NVT.Param
numberOfStates(IBox) - Method in interface etomica.tmmc.MacrostateManager: Number of expected macrostates in the box.
NumbersToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.NumbersToggler
numCarbons - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
numCarbons - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
numCarbons - Variable in class etomica.virial.ConformationAlkaneEH
numCarbons - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
numCarbons - Variable in class etomica.virial.SpeciesAlkaneEH
numCells - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
numCells - Variable in class etomica.nbr.cell.NeighborCellManager
numCellsSlider - Variable in class etomica.modules.sam.SamGraphic
numCH2 - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
numCH2 - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
numCH2 - Variable in class etomica.virial.ConformationAlkaneEH
numCH2 - Variable in class etomica.virial.SpeciesAlkaneEH
numCollapseBins - Variable in class etomica.util.HistoryCollapsing
numDelete - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
numDeleteCandidateNbrs - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
numDeleteCandidateNbrs - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
numDiagram - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
numDiagrams() - Method in class etomica.virial.ClusterChainHS
numDiagrams() - Method in class etomica.virial.ClusterChainSoft
numDiagrams() - Method in class etomica.virial.ClusterSinglyConnected
numEquilibrationSubsteps - Variable in class etomica.thermointegration.IntegratorThermodynamic
numer() - Method in class etomica.veos.bigdecimal.Rational: Get the numerator.
numerator - Variable in class etomica.util.Rational
numerator() - Method in class etomica.util.Rational: Returns the numerator.
NumericalDerivativeEnergyParacetamol - Class in etomica.paracetamol
NumericalDerivativeEnergyParacetamol(IBox, IPotentialMaster) - Constructor for class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
NumericFeature - Class in etomica.compatibility
NumericFeature(String, double) - Constructor for class etomica.compatibility.NumericFeature
numEval - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
numExtraTargetClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
NumFieldNodes - Class in etomica.graph.property: Simple class that returns the number of field nodes.
NumFieldNodes() - Constructor for class etomica.graph.property.NumFieldNodes
numH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
numH - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
numH - Variable in class etomica.virial.ConformationAlkaneEH
numH - Variable in class etomica.virial.SpeciesAlkaneEH
numIncomingValues - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
numInsert - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
numInserts - Variable in class etomica.virial.MCMoveClusterAtomHSRing
numMembraneLayers - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
numMembraneLayers - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
numMer - Variable in class etomica.association.MCMoveVolumeAssociated
numMer - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
numMol - Variable in class etomica.models.nitrogen.MeterOrientationOrderParameter
numMolec - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
numMolec - Variable in class etomica.models.nitrogen.P0LatticeEnergyCorrec
numMolecule - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
numMolecule - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
numMolecule - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
numMolecule - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
numMolecule - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
numMolecules - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
numMolecules - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.MinimizeHCP
numMolecules - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimBennet.SimBennetParam
numMolecules - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
numMolecules - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
numMolecules - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
numMolecules - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
numMolecules - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
numMolecules - Variable in class etomica.potential.EwaldSummation
numMolecules - Variable in class etomica.potential.EwaldSumMolecules
numMolecules - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
numMolecules - Variable in class etomica.virial.simulations.SimulationVirial
numMolecules - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
numMolecules - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
numMolecules - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
numMolecules - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
numMolecules - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
numMolecules - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
numMolecules - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
numMolecules - Variable in class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
numMolecules0 - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
numNeighborCandidatesOnDelete - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
numNeighborCandidatesOnDelete - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
numNeighbors - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
numNeighbors - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
numNewDeleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
numNewDeleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
numNonAdditiveNeeded - Variable in class etomica.virial.ClusterSumMultibody
numP - Variable in class etomica.normalmode.MeterDDP
numP - Variable in class etomica.normalmode.MeterDP
numP - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
NumRootNodes - Class in etomica.graph.property: Simple class that returns the number of root nodes.
NumRootNodes() - Constructor for class etomica.graph.property.NumRootNodes
numRuns - Variable in class etomica.metastable.LJmuVT.LJMCParams
numRuns - Variable in class etomica.metastable.LJNPT.LJMCParams
numRuns - Variable in class etomica.metastable.LJNVT.LJMCParams
numSteps - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
numSteps - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
numSteps - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
numSteps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
numSteps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
numSteps - Variable in class etomica.mappedvirial.MappedU.LJMDParams
numSteps - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
numSteps - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
numsteps - Variable in class etomica.meam.EFSTungsten.Params
numSteps - Variable in class etomica.metastable.LJmuVT.LJMCParams
numSteps - Variable in class etomica.metastable.LJNPT.LJMCParams
numSteps - Variable in class etomica.metastable.LJNVT.LJMCParams
numSteps - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
numSteps - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
numSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
numSteps - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
numSteps - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
numSteps - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
numSteps - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
numSteps - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
numSteps - Variable in class etomica.normalmode.SimBennet.SimBennetParam
numSteps - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
numSteps - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
numSteps - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
numSteps - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
numSteps - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
numSteps - Variable in class etomica.tests.TestHSMD3D.SimParams
numSteps - Variable in class etomica.tests.TestLJMC3D.SimParams
numSteps - Variable in class etomica.tests.TestSWChain.SimParams
numSteps - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
numSteps - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
numSteps - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
numSteps - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
numSteps - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
numSteps - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
numSteps - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
numSteps - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
numSteps - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
numSteps - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
numSteps - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
numSteps - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
numSteps - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
numSteps - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
numSteps - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
numSteps - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
numSteps - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
numSteps - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
numSteps - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
numSteps - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
numSteps - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
numSteps - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
numSteps - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
numSteps - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
numSteps - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
numSteps - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
numSteps - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
numSteps - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
numSteps - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
numSteps - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
numSteps - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
numSteps - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
numSteps - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
numSteps - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
numSteps - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
numSteps - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
numSteps - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
numSteps - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
numSteps - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
numSteps - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
numSteps - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
numSteps - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
numSteps - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
numSteps - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
numSteps - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
numSteps - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
numSteps - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
numSteps - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
numSteps - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
numSteps - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
numSteps - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
numSteps - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
numSteps - Variable in class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
numSubSteps - Variable in class etomica.overlap.IntegratorOverlap
numSubsteps - Variable in class etomica.thermointegration.IntegratorThermodynamic
numSum - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
numSum - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
numSum - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
numSum - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
numSum - Variable in class etomica.normalmode.MeterWorkTargetBennet
numSum - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
numSum - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
numSum - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
numtm - Static variable in class etomica.potential.P2WaterPotentialsJankowski
numTrial - Variable in class etomica.models.hexane.MCMoveCBMC
numTrials - Variable in class etomica.virial.MCMoveClusterAtomHSRing
numUnsafe - Variable in class etomica.nbr.list.NeighborListManager
numUpdates - Variable in class etomica.nbr.list.NeighborListManager
numV - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
numV - Variable in class etomica.normalmode.SimLJVacancy.LJParams
numWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
numXCells - Variable in class etomica.modules.sam.Sam
numZCells - Variable in class etomica.modules.sam.Sam
nValue(Token) - Static method in class org.jmol.script.ScriptVariable
nvt - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
nx - Variable in class etomica.normalmode.MeterPlaneSlip
ny - Variable in class etomica.normalmode.MeterPlaneSlip

O

obj - Variable in class etomica.util.TreeLinker
object - Variable in class etomica.graphics.DataTagBag
object - Variable in class etomica.modifier.ModifierGeneral
ObjectArrayList - Class in etomica.util: Resizable-array implementation of the List interface.
ObjectArrayList(int) - Constructor for class etomica.util.ObjectArrayList: Constructs an empty list with the specified initial capacity.
ObjectArrayList() - Constructor for class etomica.util.ObjectArrayList: Constructs an empty list.
occupancy - Static variable in class org.jmol.script.Token
occupants() - Method in class etomica.nbr.cell.Cell
occupants() - Method in class etomica.nbr.cell.molecule.CellMolecular
ochisq - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
ochisq - Variable in class etomica.util.numerical.NonLinearCurveFitting
OdeSolver - Class in etomica.util
OdeSolver() - Constructor for class etomica.util.OdeSolver
OdeSolver.Rhs - Interface in etomica.util
OdeSolver.Variables - Class in etomica.util
Oelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
off - Static variable in class org.jmol.script.Token
officialRelease - Static variable in class org.jmol.viewer.JmolConstants
offScreen - Variable in class etomica.graphics.DisplayCanvas
offset - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
offset - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
offset - Variable in class etomica.modules.sam.P1Sinusoidal
offset - Variable in class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
offset - Variable in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
offset - Variable in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
offset - Variable in class org.jmol.util.MeshSurface
offset0 - Variable in class etomica.normalmode.MeterPlaneSlip
offsetDim - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
offsetDim - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
old - Variable in class etomica.virial.ClusterChainHS
oldB - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
oldB - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
oldBondlengths - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
oldBoxSize - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
oldCenter - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
oldCenter - Variable in class etomica.virial.MCMoveClusterTorsionMulti
oldColors - Variable in class etomica.association.ColorSchemeSmer
oldDiagram - Variable in class etomica.virial.ClusterSumStickyEF
oldDirtyAtom - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
oldDirtyAtom - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
oldDirtyAtom - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
oldDirtyAtom - Variable in class etomica.virial.ClusterTree
oldEigenVectors - Variable in class etomica.normalmode.MCMoveWV
oldEnergy - Variable in class etomica.integrator.IntegratorMD
oldEpsilon - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
oldG - Variable in class etomica.modules.droplet.EllipseDisplayAction
oldGeo - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
oldGraphs - Static variable in class etomica.graph.isomorphism.Match
oldLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
oldLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
oldMu - Variable in class etomica.models.co2.PNCO2GCPM
oldMu - Variable in class etomica.models.co2.PNGCPM
oldOrientations - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
oldPartners - Variable in class etomica.potential.PotentialReactive.BondChangeData
oldPhaseAngles - Variable in class etomica.normalmode.MCMovePhaseAngle
oldPosition - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
oldPosition - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
oldPosition - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
oldPositionAgentManager - Variable in class etomica.integrator.IntegratorMD
oldPositions - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
oldPositions - Variable in class etomica.virial.MCMoveClusterRingRegrow
oldPositions - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
oldPositions - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
oldPositions - Variable in class etomica.virial.MCMoveClusterTorsionMulti
oldPotentialEnergy - Variable in class etomica.integrator.IntegratorMD
oldQ - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
oldR - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
oldSigma - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
oldStep - Variable in class etomica.modules.rosmosis.MeterFlux
oldTime - Variable in class etomica.modules.rosmosis.MeterFlux
oldTotalCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
oldValue - Variable in class etomica.modules.adsorption.ModifierPMu
oldValue - Variable in class etomica.virial.simulations.ModifierTPI
oldWaveVectors - Variable in class etomica.normalmode.MCMoveWV
OLIVE - Static variable in class org.jmol.util.Colix
omdth - Variable in class etomica.modules.rheology.IntegratorPolymer
omega() - Method in class etomica.veos.bigdecimal.Ifactor: The sum of the prime factor exponents, without multiplicity.
omega - Static variable in class org.jmol.script.Token
omega2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
omega2Table - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
omega2Table - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
omegaSquared - Variable in class etomica.normalmode.MeterHarmonicEnergy
omegaSquared - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
omegaTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
omegaTolerance - Variable in class etomica.integrator.IntegratorRigidIterative
omegaTolerance - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
ON - Static variable in class etomica.util.Debug: true if any debugging should be done
on - Static variable in class org.jmol.script.Token
ONE - Static variable in class etomica.graph.model.BitmapFactory
ONE - Static variable in class etomica.veos.bigdecimal.BigSurd: The value of one.
ONE - Static variable in class etomica.veos.bigdecimal.BigSurdVec: The value of one.
ONE - Static variable in class etomica.veos.bigdecimal.Ifactor
oneEVal - Variable in class etomica.normalmode.IntegratorHarmonic
oneIterate - Variable in class etomica.atom.iterator.MoleculeIteratorAll
oneOverSqrtOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
oneOverSqrtOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
ones - Static variable in class etomica.data.types.DataDoubleBDArray
oneWV - Variable in class etomica.normalmode.IntegratorHarmonic
onlyDoublyConnectedCB - Variable in class etomica.modules.clustergenerator.MyApplet
onlyRootPt - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
onlySinglyConnectedCB - Variable in class etomica.modules.clustergenerator.MyApplet
onlyUnique - Variable in class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
onSourceTranscodingSuccess(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController: Invoked when the rasterizer successfully transcoded the input source.
onSourceTranscodingSuccess(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.Main
onSourceTranscodingSuccess(SVGConverterSource, File) - Method in interface etomica.graph.view.rasterizer.SVGConverterController: Invoked when the rasterizer successfully transcoded the input source.
onSwitch - Variable in class etomica.models.nitrogen.PRotConstraint
OO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
OO1 - Variable in class etomica.association.BiasVolumeAceticAcid
OO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
OO2 - Variable in class etomica.association.BiasVolumeAceticAcid
oops - Variable in class etomica.models.co2.PNCO2GCPM
oops - Variable in class etomica.models.co2.PNGCPM
op - Variable in class etomica.graph.operations.UnaryChain
OPAQUE_MASK - Static variable in class org.jmol.util.Colix
open() - Method in interface etomica.graph.engine.Viewer
open() - Method in class etomica.graph.viewer.ClusterViewer
openAlkaneView() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
openFile() - Method in class etomica.zeolite.MSDCoordWriter
openFW(String) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule: Writes collected overlap data (for the "middle" alpha) to a file.
openFW(String) - Method in class etomica.normalmode.MeterTargetTP: Writes collected overlap data (for the "middle" alpha) to a file.
openSimEnvParamView() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
openStream() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
openStream() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
openStream() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource: Gets a TranscoderInput for that source
openStream() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
opEQ - Static variable in class org.jmol.script.Token
optimizeHigherbVirial(double, double) - Method in class etomica.util.numerical.B9Optimizer
optimizeHigherbVirial(int, int, double, double) - Method in class etomica.util.numerical.VirialOptimizer
optimizeRvdwWMin(P2QChemInterpolated) - Method in class etomica.potential.P2QChemInterpolated
optimizeRvdwWuTT3757(P2QChemInterpolated) - Method in class etomica.potential.P2QChemInterpolated
optionMap - Static variable in class etomica.graph.view.rasterizer.Main: Static map containing all the option handlers able to analyze the various options.
Options() - Constructor for class etomica.parser.ParserLAMMPS.Options
opToggle - Static variable in class org.jmol.script.Token
or(Bitmap) - Method in interface etomica.graph.model.Bitmap: Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap = (bitmap | other).
or(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
or(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1) for a compatible instance.
or(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
or(BitSet) - Method in class org.jmol.util.BitSet: Performs a logical OR of this bit set with the bit set argument.
or01 - Variable in class etomica.models.co2.P2CO2H2OWheatley
or01 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
or01 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
or02 - Variable in class etomica.models.co2.P2CO2H2OWheatley
or02 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
or02 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
or11 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
or11 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
or12 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
or12 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
or2 - Variable in class etomica.models.water.P2WaterSzalewicz
or3 - Variable in class etomica.potential.P3Induction
ORANGE - Static variable in class org.jmol.util.Colix
order - Variable in class etomica.virial.MayerPTAtt
order - Variable in class etomica.virial.MayerSphericalPTAtt
order - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
orderBeta - Variable in class etomica.virial.cluster.VirialDiagramsPT
org.jmol.api - package org.jmol.api
org.jmol.awt - package org.jmol.awt
org.jmol.constant - package org.jmol.constant
org.jmol.g3d - package org.jmol.g3d
org.jmol.script - package org.jmol.script
org.jmol.util - package org.jmol.util
org.jmol.viewer - package org.jmol.viewer
orH2O3 - Variable in class etomica.models.co2.P2CO2H2OWheatley
orientation - Variable in class etomica.atom.MoleculeOriented
orientation - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
orientation - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
orientation - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
Orientation2D - Class in etomica.space2d: Orientation in a 2-dimensional space.
Orientation2D() - Constructor for class etomica.space2d.Orientation2D: Default constructor sets orientation angle to zero.
Orientation2D(IVector) - Constructor for class etomica.space2d.Orientation2D: Constructs with orientation as specified by the given angle theta.
Orientation3D - Class in etomica.space3d
Orientation3D(ISpace) - Constructor for class etomica.space3d.Orientation3D: Default constructor sets orientation to point in the X direction.
OrientationAgentSource() - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
OrientationAgentSource() - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
OrientationAgentSource() - Constructor for class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
OrientationCalc - Interface in etomica.atom: Interface for a class that can calculate the orientation of a molecule or to set the orientation of a molecule.
OrientationCalcAtom - Class in etomica.atom: OrientationCalc implementation that handles a monotomic oriented molecule.
OrientationCalcAtom() - Constructor for class etomica.atom.OrientationCalcAtom
OrientationCalcQuaternion - Interface in etomica.atom: OrientationCalc interface that handles quaternions (as a a double array) instead of an Orientation object.
OrientationCalcWater3P - Class in etomica.models.water
OrientationCalcWater3P(ISpace) - Constructor for class etomica.models.water.OrientationCalcWater3P
OrientationCalcWater4P - Class in etomica.models.water
OrientationCalcWater4P(ISpace) - Constructor for class etomica.models.water.OrientationCalcWater4P
OrientationFull3D - Class in etomica.space3d
OrientationFull3D(ISpace) - Constructor for class etomica.space3d.OrientationFull3D: Default constructor sets orientation to point in the X direction.
orientationManager - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
orientationManager - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
orientationManager - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
orientationPlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
orientationProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
orientationProfilePump - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
orientationSelector - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
orientationX - Variable in class etomica.normalmode.ConformationHSDimer
OrientedAgentSource() - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
OrientedFullSite(IVector, Color, double) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
OrientedSite(double, Color, double) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
orientVector - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
originalGageLength - Variable in class etomica.modules.materialfracture.MeterElongation
originalGageLength - Variable in class etomica.modules.materialfracture.MeterStrain
origins - Variable in class etomica.space.BoundaryRectangularNonperiodic
OrnsteinZernike - Class in etomica.virial
OrnsteinZernike() - Constructor for class etomica.virial.OrnsteinZernike
ortho - Variable in class etomica.dimer.IntegratorDimerRT
ortho2 - Variable in class etomica.dimer.IntegratorDimerRT
OrthogonalPolynomial - Class in etomica.densityofstate
OrthogonalPolynomial() - Constructor for class etomica.densityofstate.OrthogonalPolynomial
osg - Variable in class etomica.graphics.DisplayCanvas
osg - Variable in class etomica.modules.clustergenerator.Plot
osg - Variable in class etomica.util.Grabber.ImagePanel
Osmosis - Class in etomica.modules.osmosis: Osmosis module.
Osmosis(OsmosisSim, ISpace) - Constructor for class etomica.modules.osmosis.Osmosis
Osmosis.Applet - Class in etomica.modules.osmosis
Osmosis.InitializeMolecules - Class in etomica.modules.osmosis
Osmosis.MyWall - Class in etomica.modules.osmosis
osmosisPMeter - Variable in class etomica.modules.osmosis.Osmosis
OsmosisSim - Class in etomica.modules.osmosis: Osmosis simulation.
OsmosisSim(Space) - Constructor for class etomica.modules.osmosis.OsmosisSim
otherAngles - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
otherAngles - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
otherAngles - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
otherDensities - Variable in class etomica.normalmode.MeterDDP
otherDensities - Variable in class etomica.normalmode.MeterDP
otherFrac - Variable in class etomica.normalmode.MeterOverlapSwitch
otherFrac - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
otherPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
otherRho - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
otherSpecies - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
otherTemperature - Variable in class etomica.normalmode.MeterBoltzmannHTTP
otherTemperatures - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
otherTemperatures - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
otherTemperatures - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
otherTemperatures - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
otherTemperatures - Variable in class etomica.normalmode.MeterTargetTP
otherTemperatures - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
otherTemperatures - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
otherTemperatures - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
oType - Variable in class etomica.models.rowley.SpeciesEthanol
oType - Variable in class etomica.models.rowley.SpeciesMethanol
oType - Variable in class etomica.models.traPPE.SpeciesMethanol
oType - Variable in class etomica.models.water.SpeciesWater3P
oType - Variable in class etomica.models.water.SpeciesWater3POriented
oType - Variable in class etomica.models.water.SpeciesWater4P
oType - Variable in class etomica.models.water.SpeciesWater4PCOM
oType - Variable in class etomica.models.water.SpeciesWater4POriented
oType - Variable in class etomica.paracetamol.SpeciesParacetamol
oType - Variable in class etomica.virial.SpeciesTraPPECO2
out - Variable in class etomica.metastable.LJmuVT.LJMCParams
out - Variable in class etomica.metastable.LJNPT.LJMCParams
out - Variable in class etomica.metastable.LJNVT.LJMCParams
outData - Variable in class etomica.data.DataDistributer
outData - Variable in class etomica.data.DataGroupSplitter
outData - Variable in class etomica.data.DataSplitter
outDegree - Variable in class etomica.virial.ClusterSumHS
outDegree - Variable in class etomica.virial.ClusterWheatleyHS
outDegree - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
outDegreeCore - Variable in class etomica.virial.ClusterWheatleyExtendSW
outDegreeWell - Variable in class etomica.virial.ClusterWheatleyExtendSW
outNData - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
outNDataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
output() - Method in class etomica.math.linearalgebra.EigenSystemReduction
output() - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
output - Variable in class etomica.modules.clustergenerator.MyApplet
outputArea - Variable in class etomica.util.Grabber
outputfilename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
outputname - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
outputname - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
outputname - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
outputname - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
outputname - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
outputname - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
outputname - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
outputname - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
outRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
oValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
OverflowShift - Class in etomica.graphics
overlapAvgA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
overlapAvgB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
overlapBlockCovSum - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
overlapCorrelationSum - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
overlapFirstBlock - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
overlapMostRecentBlock - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
Oxygen - Class in etomica.chem.elements: Class for the Oxygen element.
Oxygen(String) - Constructor for class etomica.chem.elements.Oxygen
Oxygen(String, double) - Constructor for class etomica.chem.elements.Oxygen
oy - Variable in class etomica.util.numerical.AkimaSplineSmoother

P

P - Variable in class etomica.atom.iterator.ANIntergroupExchange
P - Variable in class etomica.atom.iterator.ANIntragroupExchange
P - Variable in class etomica.atom.iterator.ApiIntergroupExchange
p - Variable in class etomica.box.RandomPositionSourceDeformable
p - Variable in class etomica.box.RandomPositionSourceRectangular
p - Variable in class etomica.normalmode.MeterDDP
p - Variable in class etomica.normalmode.MeterDP
p - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
P - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
P - Variable in class etomica.potential.P2HePCKLJS
p - Variable in class etomica.potential.P2HydrogenPatkowski
p - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
p - Variable in class etomica.potential.PotentialAtomicSum
p - Variable in class etomica.potential.PotentialMolecularSum
p - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
p - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
p - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
p - Variable in class etomica.virial.cluster.VirialDiagrams
p - Variable in class etomica.virial.cluster.VirialDiagramsMix
p - Variable in class etomica.virial.cluster.VirialDiagramsMix2
p - Variable in class etomica.virial.cluster.VirialDiagramsPT
p - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
p - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
P - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
p - Variable in class etomica.virial.PotentialNonAdditive
p0 - Variable in class etomica.virial.MCMoveClusterAtomHSRing
P0LatticeEnergyCorrec - Class in etomica.models.nitrogen: The lattice energy correction for Nitrogen model zero-body interaction All the parameters are determined from the fitted equation.
P0LatticeEnergyCorrec(ISpace) - Constructor for class etomica.models.nitrogen.P0LatticeEnergyCorrec
P0Lrc(ISpace, Potential2Soft, Potential2Soft, IAtomType[]) - Constructor for class etomica.potential.P2SoftSphericalTruncated.P0Lrc
P0ReactionField(ISpace, P2ReactionFieldDipole) - Constructor for class etomica.potential.P2ReactionFieldDipole.P0ReactionField
P0ReactionField(ISpace, P2ReactionFieldDipoleTruncated) - Constructor for class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomNPath
p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
p1 - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
p1 - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
p1 - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
p1 - Variable in class etomica.normalmode.MeterBoltzmannHTTP
p1 - Variable in class etomica.normalmode.MeterDDP
p1 - Variable in class etomica.normalmode.MeterDP
p1 - Variable in class etomica.normalmode.MeterTargetTP
p1 - Variable in class etomica.potential.P2HydrogenPatkowski
p1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
p1 - Variable in class etomica.virial.ClusterExchange
p1 - Variable in class etomica.virial.P1IntraLambda
p1BoundaryA - Variable in class etomica.modules.mu.Mu
p1BoundaryB - Variable in class etomica.modules.mu.Mu
p1Constraint - Variable in class etomica.normalmode.HTTPSoftSphereSim
P1Constraint - Class in etomica.normalmode
P1Constraint(ISpace, double, IBox, CoordinateDefinition) - Constructor for class etomica.normalmode.P1Constraint
p1Constraint - Variable in class etomica.normalmode.SimCalcSLJ
p1Constraint - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
p1Constraint - Variable in class etomica.normalmode.SimOverlapLJ
p1Constraint - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
p1Constraint - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
P1ConstraintNbr - Class in etomica.normalmode
P1ConstraintNbr(ISpace, double, ISimulation) - Constructor for class etomica.normalmode.P1ConstraintNbr
P1ConstraintNbr(ISpace, double, ISimulation, double) - Constructor for class etomica.normalmode.P1ConstraintNbr
P1ConstraintNbrHcp - Class in etomica.normalmode
P1ConstraintNbrHcp(ISpace, double, IBox) - Constructor for class etomica.normalmode.P1ConstraintNbrHcp
p1Counter - Variable in class etomica.normalmode.P1ConstraintNbrHcp
P1ExternalField - Class in etomica.potential
P1ExternalField(ISpace) - Constructor for class etomica.potential.P1ExternalField
P1HardBoundary - Class in etomica.potential: Potential that places hard repulsive walls coinciding with the boundary of the box, which is assumed to be rectangular in shape.
P1HardBoundary(ISpace) - Constructor for class etomica.potential.P1HardBoundary
P1HardBoundary(ISpace, boolean) - Constructor for class etomica.potential.P1HardBoundary
P1HardMovingBoundary - Class in etomica.potential: Potential that places hard repulsive walls that move and accelerate subject to an external force field (pressure).
P1HardMovingBoundary(ISpace, IBoundary, int, double, boolean) - Constructor for class etomica.potential.P1HardMovingBoundary: Constructor for a hard moving (and accelerating) boundary.
P1HardPeriodic - Class in etomica.potential: pseudo-potential for a "collision" time to update colliders for periodic boundaries
P1HardPeriodic(ISpace) - Constructor for class etomica.potential.P1HardPeriodic: Returns an instance of P1HardPeriodic with sigma = NaN.
P1HardPeriodic(ISpace, double) - Constructor for class etomica.potential.P1HardPeriodic: Returns an instance of P1HardPeriodic with the given value of sigma (the maximum distance between two atoms where they interact)
P1HardWall - Class in etomica.modules.osmosis
P1HardWall(ISpace) - Constructor for class etomica.modules.osmosis.P1HardWall
P1HardWall(ISpace, double) - Constructor for class etomica.modules.osmosis.P1HardWall
P1Harmonic - Class in etomica.potential: Potential in which attaches a harmonic spring between each affected atom and the nearest boundary in each direction.
P1Harmonic(ISpace) - Constructor for class etomica.potential.P1Harmonic
P1HarmonicSite - Class in etomica.potential: Potential in which attaches a harmonic spring between each affected atom a nominal site for that atom, as defined by an agent manager.
P1HarmonicSite(ISpace) - Constructor for class etomica.potential.P1HarmonicSite
P1HydrogenMielke - Class in etomica.potential
P1HydrogenMielke(ISpace) - Constructor for class etomica.potential.P1HydrogenMielke
P1HydrogenMielke.P1HydrogenMielkeAtomic - Class in etomica.potential
P1HydrogenMielke.P2HydrogenMielkeAtomic - Class in etomica.potential
P1HydrogenMielkeAtomic(ISpace) - Constructor for class etomica.potential.P1HydrogenMielke.P1HydrogenMielkeAtomic
P1ImageHarmonic - Class in etomica.freeenergy.npath: Created by andrew on 4/11/17.
P1ImageHarmonic(ISpace, IVector, double) - Constructor for class etomica.freeenergy.npath.P1ImageHarmonic
p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimIdealGas
p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimLJ
p1Intra - Variable in class etomica.modules.sam.Sam
P1IntraLambda - Class in etomica.virial
P1IntraLambda(ISpace, double, P1IntraMolecular, double) - Constructor for class etomica.virial.P1IntraLambda
P1IntraMolecular - Interface in etomica.potential
P1IntraSimple - Class in etomica.potential: Generic intramolecular potential group, having one potential for bonded atoms, and a different potential for unbonded ones.
P1IntraSimple() - Constructor for class etomica.potential.P1IntraSimple
P1LepsHarmonic - Class in etomica.dimer: A combination of the basic LEPS potential describing 3 atoms moving in 1-dimension, paired with a harmonic potential.
P1LepsHarmonic(ISpace) - Constructor for class etomica.dimer.P1LepsHarmonic
P1MagicWall - Class in etomica.modules.mu
P1MagicWall(ISpace, PotentialMasterList) - Constructor for class etomica.modules.mu.P1MagicWall
P1MagneticField - Class in etomica.spin: TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates
P1MagneticField(ISpace) - Constructor for class etomica.spin.P1MagneticField
P1Sinusoidal - Class in etomica.modules.sam
P1Sinusoidal(ISpace) - Constructor for class etomica.modules.sam.P1Sinusoidal
p1Smash - Variable in class etomica.modules.droplet.Droplet
p1Smash - Variable in class etomica.modules.droplet.DropletAtomic
P1Smash - Class in etomica.modules.droplet: Gravity-like potential that pushes the molecules toward the center.
P1Smash(ISpace) - Constructor for class etomica.modules.droplet.P1Smash
P1SoftBoundary - Class in etomica.potential
P1SoftBoundary(ISpace) - Constructor for class etomica.potential.P1SoftBoundary
P1SoftBoundary(ISpace, double) - Constructor for class etomica.potential.P1SoftBoundary
p1SurfaceBond - Variable in class etomica.modules.sam.Sam
p1Tension - Variable in class etomica.modules.materialfracture.MaterialFracture
P1Tension - Class in etomica.modules.materialfracture
P1Tension(ISpace) - Constructor for class etomica.modules.materialfracture.P1Tension
P1Tether - Class in etomica.modules.rosmosis: Potential for a harmonic tether.
P1Tether(IBox, ISpecies, ISpace) - Constructor for class etomica.modules.rosmosis.P1Tether
P1Wall - Class in etomica.interfacial
P1Wall(ISpace, double, double, double) - Constructor for class etomica.interfacial.P1Wall
P1Wall - Class in etomica.modules.adsorption
P1Wall(ISpace) - Constructor for class etomica.modules.adsorption.P1Wall
P1Wall - Class in etomica.modules.colloid
P1Wall(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P1Wall
p1WallA - Variable in class etomica.modules.adsorption.Adsorption
p1WallA - Variable in class etomica.modules.mu.Mu
p1WallB - Variable in class etomica.modules.adsorption.Adsorption
p1WallB - Variable in class etomica.modules.mu.Mu
p1WallColloid - Variable in class etomica.modules.colloid.ColloidSim
p1WallMonomer - Variable in class etomica.modules.colloid.ColloidSim
P1WCAPorousWall - Class in etomica.modules.dcvgcmd: This acts as a 1-body WCA potential wall perpendicular to the z direction with a hole.
P1WCAPorousWall(ISpace) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
P1WCAPorousWall(ISpace, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
P1WCAWall - Class in etomica.modules.dcvgcmd: 1-D potential that has a WCA form in the Z direction.
P1WCAWall(ISpace, int) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
P1WCAWall(ISpace, int, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
P1WCAWall - Class in etomica.modules.sam: 1-D potential that has a WCA form in the Z direction.
P1WCAWall(ISpace, int) - Constructor for class etomica.modules.sam.P1WCAWall
P1WCAWall(ISpace, int, double, double) - Constructor for class etomica.modules.sam.P1WCAWall
p2 - Variable in class etomica.mappedvirial.MeterMeanForce
p2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
p2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
p2 - Variable in class etomica.metastable.MeterDensityDistribution
p2 - Variable in class etomica.modules.adsorption.ModifierPMu
p2 - Variable in class etomica.modules.droplet.Droplet
p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
p2 - Variable in class etomica.potential.P2HydrogenPatkowski
p2 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
p2 - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
p2 - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
P22CLJQ - Class in etomica.potential: Two-centered Lennard Jones molecule with a quadrupole.
P22CLJQ(ISpace) - Constructor for class etomica.potential.P22CLJQ
P22CLJQ(ISpace, double, double, double) - Constructor for class etomica.potential.P22CLJQ
p2AA - Variable in class etomica.modules.adsorption.Adsorption
p2AA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
p2AA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
p2AB - Variable in class etomica.modules.adsorption.Adsorption
p2AB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
P2AceticAcidTwoSite - Class in etomica.models.OPLS
P2AceticAcidTwoSite(double, boolean, int) - Constructor for class etomica.models.OPLS.P2AceticAcidTwoSite
P2Anharmonic - Class in etomica.potential: Harmonic Well interatomic potential.
P2Anharmonic(ISpace, double) - Constructor for class etomica.potential.P2Anharmonic
P2ArgonAziz1993 - Class in etomica.potential: Pair potential for argon from Aziz (1993) JCP 99(6): 4518.
P2ArgonAziz1993(ISpace) - Constructor for class etomica.potential.P2ArgonAziz1993
P2ArgonSlavicekEtAl2003 - Class in etomica.potential: Ab initio pair potential for argon from Slavicek et al.
P2ArgonSlavicekEtAl2003(ISpace) - Constructor for class etomica.potential.P2ArgonSlavicekEtAl2003
P2ArgonTangAndToennies2003 - Class in etomica.potential: Pair potential for argon from Tang and Toennies 2003.
P2ArgonTangAndToennies2003(ISpace) - Constructor for class etomica.potential.P2ArgonTangAndToennies2003
p2BB - Variable in class etomica.modules.adsorption.Adsorption
p2BB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
p2BB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
p2Bond - Variable in class etomica.modules.interfacial.InterfacialSW
p2BondCC - Variable in class etomica.modules.sam.Sam
p2BondCS - Variable in class etomica.modules.sam.Sam
p2CH2 - Variable in class etomica.modules.sam.Sam
p2CH2CH3 - Variable in class etomica.modules.sam.Sam
p2CH2CH3t - Variable in class etomica.modules.sam.Sam
p2CH2Surface - Variable in class etomica.modules.sam.Sam
p2CH2t - Variable in class etomica.modules.sam.Sam
p2CH3 - Variable in class etomica.modules.sam.Sam
p2CH3t - Variable in class etomica.modules.sam.Sam
p2Classy - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
p2Classy - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
p2Classy - Variable in class etomica.potential.P2SemiclassicalAtomic
p2Classy - Variable in class etomica.potential.P2SemiclassicalMolecular
P2CO2EMP - Class in etomica.potential: 3-point potential for CO2.
P2CO2EMP(ISpace, double, double, double, double, double, double, double) - Constructor for class etomica.potential.P2CO2EMP
P2CO2EMP1 - Class in etomica.potential: EPM model for CO2.
P2CO2EMP1(ISpace) - Constructor for class etomica.potential.P2CO2EMP1
P2CO2EMP2 - Class in etomica.potential: EPM2 model for CO2
P2CO2EMP2(ISpace) - Constructor for class etomica.potential.P2CO2EMP2
P2CO2H2OSC(double) - Constructor for class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
P2CO2H2OSCTI(double) - Constructor for class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
P2CO2H2OWheatley - Class in etomica.models.co2: Ab initio potential for CO2-H2O by Wheatley and Harvey http://dx.doi.org/10.1063/1.3574345 The CO2 molecule is expected first
P2CO2H2OWheatley(ISpace) - Constructor for class etomica.models.co2.P2CO2H2OWheatley
P2CO2H2OWheatley.P2CO2H2OSC - Class in etomica.models.co2
P2CO2H2OWheatley.P2CO2H2OSCTI - Class in etomica.models.co2
P2CO2Hellmann - Class in etomica.models.co2: Ab initio potential for CO2-CO2 developed by R.
P2CO2Hellmann(ISpace, P2CO2Hellmann.Parameters) - Constructor for class etomica.models.co2.P2CO2Hellmann
P2CO2Hellmann.P2CO2SC - Class in etomica.models.co2
P2CO2Hellmann.Parameters - Enum in etomica.models.co2
P2CO2SC(double) - Constructor for class etomica.models.co2.P2CO2Hellmann.P2CO2SC
P2CO2TraPPE - Class in etomica.potential: I used this original EPM2model to describe TraPPECO2 model the two models are different in parameters.
P2CO2TraPPE(ISpace) - Constructor for class etomica.potential.P2CO2TraPPE
P2Cohesion - Class in etomica.modules.droplet: Cohesive potential for mesoscale droplet simulation
P2Cohesion(ISpace) - Constructor for class etomica.modules.droplet.P2Cohesion
P2DiscreteFeynmanHibbs - Class in etomica.potential: Effective 2 body potential approximating the quantum behavior of atomic interactions.
P2DiscreteFeynmanHibbs(ISpace, Potential2Spherical) - Constructor for class etomica.potential.P2DiscreteFeynmanHibbs
P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum - Class in etomica.potential
P2DLPOLY - Class in etomica.potential
P2DLPOLY(ISpace) - Constructor for class etomica.potential.P2DLPOLY
P2DoubleWell - Class in etomica.potential: Double-well potential.
P2DoubleWell(ISpace) - Constructor for class etomica.potential.P2DoubleWell
P2DoubleWell(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2DoubleWell
P2Dreiding - Class in etomica.potential: Dreiding potential.
P2Dreiding(ISpace, double, double) - Constructor for class etomica.potential.P2Dreiding
P2EffectiveFeynmanHibbs - Class in etomica.potential: Effective 2 body potential approximating the quantum behavior of atomic interactions.
P2EffectiveFeynmanHibbs(ISpace, Potential2SoftSpherical) - Constructor for class etomica.potential.P2EffectiveFeynmanHibbs
P2Electrostatic - Class in etomica.potential: Simple electrostatic potential class.
P2Electrostatic(ISpace) - Constructor for class etomica.potential.P2Electrostatic
P2ElectrostaticDreiding - Class in etomica.paracetamol: Empirical Isotropic atom-atom repulsion-dispersion potential Given formula: U(r) = A*exp(-r/B) - C /r^6 A is in eV B is in angstrom C is in eV.angstrom^6
P2ElectrostaticDreiding(ISpace) - Constructor for class etomica.paracetamol.P2ElectrostaticDreiding
P2ElectrostaticDreiding(ISpace, double, double, double) - Constructor for class etomica.paracetamol.P2ElectrostaticDreiding
P2ElectrostaticWithHardCore - Class in etomica.potential: Simple electrostatic potential class.
P2ElectrostaticWithHardCore(ISpace) - Constructor for class etomica.potential.P2ElectrostaticWithHardCore
P2EwaldReal() - Constructor for class etomica.potential.EwaldSummation.P2EwaldReal
P2Exp6 - Class in etomica.potential: Exponential-6 atom-atom repulsion-dispersion potential.
P2Exp6(ISpace) - Constructor for class etomica.potential.P2Exp6
P2Exp6(ISpace, double, double, double) - Constructor for class etomica.potential.P2Exp6
P2Exp6Buckingham - Class in etomica.potential: The Buckingham Exponential-6 atom-atom dispersion potential.
P2Exp6Buckingham(ISpace) - Constructor for class etomica.potential.P2Exp6Buckingham
P2Exp6Buckingham(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2Exp6Buckingham
P2Fene - Class in etomica.potential: Finite elastic nonlinear extensible (FENE) spring potential.
P2Fene(ISpace) - Constructor for class etomica.potential.P2Fene
P2Fene(ISpace, double, double) - Constructor for class etomica.potential.P2Fene
P2H2OSC(double) - Constructor for class etomica.models.water.P2WaterSzalewicz.P2H2OSC
P2HardAssociation - Class in etomica.potential: Purely attractive square-well potential with no repulsive core.
P2HardAssociation(ISpace) - Constructor for class etomica.potential.P2HardAssociation
P2HardAssociation(ISpace, double, double) - Constructor for class etomica.potential.P2HardAssociation
P2HardAssociationCone - Class in etomica.potential: Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationCone(ISpace) - Constructor for class etomica.potential.P2HardAssociationCone
P2HardAssociationCone(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationCone
P2HardAssociationConeDoubleSites - Class in etomica.potential: Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationConeDoubleSites(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeDoubleSites
P2HardAssociationConeFourSites - Class in etomica.potential: Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationConeFourSites(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeFourSites
P2HardAssociationConeFourSitesSW - Class in etomica.potential: Square-Well cone of attraction for associating fluid theory Four association sites
P2HardAssociationConeFourSitesSW(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeFourSitesSW
P2HardAssociationConeOneSite - Class in etomica.potential: Lennard-Jones potential with a square-well cone of attraction.
P2HardAssociationConeOneSite(ISpace) - Constructor for class etomica.potential.P2HardAssociationConeOneSite
P2HardAssociationConeOneSite(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeOneSite
P2HardAssociationConeReference - Class in etomica.potential: potential with a square-well cone of attraction for reference system.
P2HardAssociationConeReference(ISpace, double) - Constructor for class etomica.potential.P2HardAssociationConeReference
P2HardAssociationConeReferenceFourSites - Class in etomica.potential: potential with a square-well cone of attraction for reference system.
P2HardAssociationConeReferenceFourSites(ISpace, double) - Constructor for class etomica.potential.P2HardAssociationConeReferenceFourSites
P2HardAssociationConeSW - Class in etomica.potential: Square-Well cone of attraction for associating fluid theory double association sites
P2HardAssociationConeSW(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeSW
P2HardAssociationGCPMReference - Class in etomica.models.water
P2HardAssociationGCPMReference(ISpace, boolean) - Constructor for class etomica.models.water.P2HardAssociationGCPMReference
P2HardAssociationRefAceticAcidTwoSite - Class in etomica.models.OPLS
P2HardAssociationRefAceticAcidTwoSite() - Constructor for class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
P2HardBond - Class in etomica.potential: Potential that acts like a hard string connecting the centers of two atoms.
P2HardBond(ISpace) - Constructor for class etomica.potential.P2HardBond
P2HardBond(ISpace, double, double, boolean) - Constructor for class etomica.potential.P2HardBond
P2HardBondedList - Class in etomica.potential: Hard potential that wraps two others.
P2HardBondedList(Simulation, PotentialHard, PotentialHard) - Constructor for class etomica.potential.P2HardBondedList
P2HardBondedList.BondArrayList - Class in etomica.potential
P2HardSphere - Class in etomica.potential: Basic hard-(rod/disk/sphere) potential.
P2HardSphere(ISpace) - Constructor for class etomica.potential.P2HardSphere
P2HardSphere(ISpace, double, boolean) - Constructor for class etomica.potential.P2HardSphere
P2HardSphereMC - Class in etomica.modules.colloid
P2HardSphereMC(ISpace, AtomLeafAgentManager<? extends IAtomList>) - Constructor for class etomica.modules.colloid.P2HardSphereMC
P2HardWrapper - Class in etomica.potential: Hard potential class that wraps another hard potential.
P2HardWrapper(ISpace, PotentialHard) - Constructor for class etomica.potential.P2HardWrapper
P2Harmonic - Class in etomica.potential: Harmonic Well interatomic potential.
P2Harmonic(ISpace, double) - Constructor for class etomica.potential.P2Harmonic
P2Harmonic(ISpace, double, double) - Constructor for class etomica.potential.P2Harmonic
P2HC2Yukawa - Class in etomica.yukawa: Hard-core plus two Yukawa fluid (HC2Yukawa): A Lennard-Jones like potential.
P2HC2Yukawa(ISpace) - Constructor for class etomica.yukawa.P2HC2Yukawa
P2HC2Yukawa(ISpace, double, double) - Constructor for class etomica.yukawa.P2HC2Yukawa
p2Head - Variable in class etomica.modules.interfacial.InterfacialSW
p2HeadHead - Variable in class etomica.modules.interfacial.InterfacialSW
p2HeadTail - Variable in class etomica.modules.interfacial.InterfacialSW
P2HeEmpericalQuantum(ISpace, P2HePCKLJS, double) - Constructor for class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
P2HePCKLJS - Class in etomica.potential: Ab initio pair potential for helium from Przybytek et al.
P2HePCKLJS(ISpace) - Constructor for class etomica.potential.P2HePCKLJS
P2HePCKLJS(ISpace, double) - Constructor for class etomica.potential.P2HePCKLJS
P2HePCKLJS.P2HeQFH - Class in etomica.potential: This inner class can calculates the Feynman-Hibbs semiclassical approximation for the potential.
P2HePCKLJS.P2HeTI - Class in etomica.potential
P2HeQFH(double) - Constructor for class etomica.potential.P2HePCKLJS.P2HeQFH
P2HeQFH(double) - Constructor for class etomica.potential.P2HeSimplified.P2HeQFH
P2HeSimplified - Class in etomica.potential: Simplified pair potential for Helium.
P2HeSimplified(ISpace) - Constructor for class etomica.potential.P2HeSimplified
P2HeSimplified.P2HeQFH - Class in etomica.potential: This inner class can calculates the Feynman-Hibbs semiclassical approximation for the potential.
P2HeSimplified.P2HeTI - Class in etomica.potential
P2HeTI(double) - Constructor for class etomica.potential.P2HePCKLJS.P2HeTI
P2HeTI(double) - Constructor for class etomica.potential.P2HeSimplified.P2HeTI
p2Hinde - Variable in class etomica.potential.P2HydrogenHindePatkowski
p2Hinde - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
P2HSDipole - Class in etomica.potential: Hard sphere molecule with a dipole sitting at the center.
P2HSDipole(ISpace) - Constructor for class etomica.potential.P2HSDipole
P2HSDipole(ISpace, double) - Constructor for class etomica.potential.P2HSDipole
P2HSDipole(ISpace, double, double) - Constructor for class etomica.potential.P2HSDipole
P2HSDipole(ISpace, double, double, double) - Constructor for class etomica.potential.P2HSDipole
P2HydrogenHinde - Class in etomica.potential
P2HydrogenHinde(ISpace) - Constructor for class etomica.potential.P2HydrogenHinde
P2HydrogenHinde.P2HydrogenHindeAtomic - Class in etomica.potential
P2HydrogenHinde.P2HydrogenHindeMolecular - Class in etomica.potential
P2HydrogenHindeAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHinde.P2HydrogenHindeAtomic
P2HydrogenHindeAtomic - Class in etomica.potential
P2HydrogenHindeAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHindeAtomic
P2HydrogenHindeMolecular(ISpace) - Constructor for class etomica.potential.P2HydrogenHinde.P2HydrogenHindeMolecular
P2HydrogenHindePatkowski - Class in etomica.potential
P2HydrogenHindePatkowski(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowski
P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic - Class in etomica.potential
P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular - Class in etomica.potential
P2HydrogenHindePatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic
P2HydrogenHindePatkowskiAtomic - Class in etomica.potential
P2HydrogenHindePatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowskiAtomic
P2HydrogenHindePatkowskiMolecular(ISpace) - Constructor for class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular
P2HydrogenMielkeAtomic(ISpace) - Constructor for class etomica.potential.P1HydrogenMielke.P2HydrogenMielkeAtomic
P2HydrogenPatkowski - Class in etomica.potential
P2HydrogenPatkowski(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowski
P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic - Class in etomica.potential
P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular - Class in etomica.potential
P2HydrogenPatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic
P2HydrogenPatkowskiAtomic - Class in etomica.potential
P2HydrogenPatkowskiAtomic(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowskiAtomic
P2HydrogenPatkowskiIso - Class in etomica.potential
P2HydrogenPatkowskiIso(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowskiIso
P2HydrogenPatkowskiMolecular(ISpace) - Constructor for class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular
P2Ideal - Class in etomica.potential: Ideal-gas two-body potential, which defines no interactions and zero energy for all pairs given to it.
P2Ideal(ISpace) - Constructor for class etomica.potential.P2Ideal
P2LennardJones - Class in etomica.potential: Lennard-Jones interatomic potential.
P2LennardJones(ISpace) - Constructor for class etomica.potential.P2LennardJones
P2LennardJones(ISpace, double, double) - Constructor for class etomica.potential.P2LennardJones
P2LennardJonesDreiding - Class in etomica.potential: Dreiding: Lennard-Jones non-bonding potential.
P2LennardJonesDreiding(ISpace) - Constructor for class etomica.potential.P2LennardJonesDreiding
P2LennardJonesDreiding(ISpace, double, double) - Constructor for class etomica.potential.P2LennardJonesDreiding
p2LJ - Variable in class etomica.modules.droplet.DropletAtomic
p2LJ - Variable in class etomica.modules.materialfracture.MaterialFracture
p2LJ - Variable in class etomica.normalmode.SimLJVacancy
p2lj - Variable in class etomica.threaded.atom.LJMD3DThreaded
p2lj - Variable in class etomica.threaded.domain.LJMD3DThreaded
P2LJDipole - Class in etomica.potential: Lennard Jones molecule with a point dipole sitting in the center.
P2LJDipole(ISpace, double, double, double, double) - Constructor for class etomica.potential.P2LJDipole
P2LJDipole - Class in etomica.rotation: r^-12 potential plus a point dipole, force shifted, as used in Kol, Laird and Leimkuhler, JCP 107 (1997) 2580-2588.
P2LJDipole(ISpace) - Constructor for class etomica.rotation.P2LJDipole
P2LJDipole(ISpace, double, double, double) - Constructor for class etomica.rotation.P2LJDipole
p2LJQ - Variable in class etomica.modules.vle.VLESim
P2LJQ - Class in etomica.potential: Lennard Jones molecule with a quadrupole.
P2LJQ(ISpace) - Constructor for class etomica.potential.P2LJQ
P2LJQ(ISpace, double, double, double) - Constructor for class etomica.potential.P2LJQ
P2LJQQ - Class in etomica.potential: Lennard Jones molecule with a quadrupole.
P2LJQQ(ISpace) - Constructor for class etomica.potential.P2LJQQ
P2LJQQ(ISpace, double, double, double) - Constructor for class etomica.potential.P2LJQQ
p2LJt - Variable in class etomica.modules.droplet.DropletAtomic
p2mc - Variable in class etomica.modules.colloid.ColloidSim
p2mc - Variable in class etomica.modules.colloid.NeighborListManagerColloid
p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
p2mm - Variable in class etomica.modules.colloid.ColloidSim
P2ModifiedMorse - Class in etomica.potential
P2ModifiedMorse(ISpace) - Constructor for class etomica.potential.P2ModifiedMorse
P2ModifiedMorse(ISpace, double, double, double, double, double, double) - Constructor for class etomica.potential.P2ModifiedMorse
P2MoleculeMonatomic - Class in etomica.potential
P2MoleculeMonatomic(IPotentialAtomic) - Constructor for class etomica.potential.P2MoleculeMonatomic
P2MoleculeSoftTruncatedSwitched - Class in etomica.potential: Wraps a soft-spherical potential to apply a truncation to it.
P2MoleculeSoftTruncatedSwitched(IPotentialMolecularTorque, double, ISpace) - Constructor for class etomica.potential.P2MoleculeSoftTruncatedSwitched
P2MoleculeTruncated - Class in etomica.potential: Wraps a soft-spherical potential to apply a truncation to it.
P2MoleculeTruncated(IPotentialMolecular, double, ISpace, IAtomPositionDefinition) - Constructor for class etomica.potential.P2MoleculeTruncated
P2Morse - Class in etomica.potential
P2Morse(ISpace) - Constructor for class etomica.potential.P2Morse
P2Morse(ISpace, double, double, double) - Constructor for class etomica.potential.P2Morse
p2N2HellmannA - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
P2N2QFH(double) - Constructor for class etomica.potential.P2NitrogenHellmann.P2N2QFH
P2Nitrogen - Class in etomica.models.nitrogen: P2 6-point potential for Nitrogen.
P2Nitrogen(ISpace, double) - Constructor for class etomica.models.nitrogen.P2Nitrogen
P2NitrogenAB - Class in etomica.models.nitrogen: P2 6-point potential for Nitrogen.
P2NitrogenAB(ISpace, double) - Constructor for class etomica.models.nitrogen.P2NitrogenAB
P2NitrogenAnisotropic - Class in etomica.models.nitrogen: P2 6-point potential for Nitrogen with anisotropic contribution Reference: 1.
P2NitrogenAnisotropic(ISpace, double) - Constructor for class etomica.models.nitrogen.P2NitrogenAnisotropic
P2NitrogenHellmann - Class in etomica.potential
P2NitrogenHellmann(ISpace) - Constructor for class etomica.potential.P2NitrogenHellmann
P2NitrogenHellmann.P2N2QFH - Class in etomica.potential
P2NitrogenShellModel - Class in etomica.models.nitrogen: CAUTION!!!!!! The potential DOES NOT really describe the ALPHA and GAMMA structure at NON-ZERO temperature condition!! (through observation [SimulationGraphic] and pressure calculation[MeterPressureMolecular]) P2 shell-model potential for Nitrogen.
P2NitrogenShellModel(ISpace, double) - Constructor for class etomica.models.nitrogen.P2NitrogenShellModel
P2O2Bartolomei - Class in etomica.potential
P2O2Bartolomei(ISpace) - Constructor for class etomica.potential.P2O2Bartolomei
P2O2Bartolomei.P2O2TI - Class in etomica.potential
P2O2TI(double) - Constructor for class etomica.potential.P2O2Bartolomei.P2O2TI
p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
p2Patkowski - Variable in class etomica.potential.P2HydrogenHindePatkowski
p2Patkowski - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
P2PenetrableBond - Class in etomica.potential: Potential with a well having a finite potential on either side.
P2PenetrableBond(ISpace) - Constructor for class etomica.potential.P2PenetrableBond
P2PenetrableBond(ISpace, double, double, boolean) - Constructor for class etomica.potential.P2PenetrableBond
P2PenetrableCar(ISpace, ParseObj, IBox) - Constructor for class etomica.modules.render.RenderMD.P2PenetrableCar
P2PenetrableSphere - Class in etomica.potential: Basic penetrable-sphere potential.
P2PenetrableSphere(ISpace) - Constructor for class etomica.potential.P2PenetrableSphere: Constructor with default values of unity for core diameter and core energy.
P2PenetrableSphere(ISpace, double, double) - Constructor for class etomica.potential.P2PenetrableSphere
P2PenetrableSquareWell - Class in etomica.potential: Square-well potential with a penetrable core.
P2PenetrableSquareWell(ISpace) - Constructor for class etomica.potential.P2PenetrableSquareWell
P2PenetrableSquareWell(ISpace, double, double, double, boolean) - Constructor for class etomica.potential.P2PenetrableSquareWell
p2pseudo - Variable in class etomica.modules.colloid.ColloidSim
p2pseudo - Variable in class etomica.modules.colloid.NeighborListManagerColloid
P2QChem - Class in etomica.potential: This class requires a bash script called ./runQChem to load the appropriate Q-Chem module and run it.
P2QChem(ISpace) - Constructor for class etomica.potential.P2QChem
P2QChemInterpolated - Class in etomica.potential: Pair potential for argon interpolated from Q-Chem results.
P2QChemInterpolated(ISpace) - Constructor for class etomica.potential.P2QChemInterpolated
P2QChemInterpolated.DampingParams - Class in etomica.potential
P2ReactionFieldDipole - Class in etomica.potential
P2ReactionFieldDipole(ISpace, IAtomPositionDefinition) - Constructor for class etomica.potential.P2ReactionFieldDipole
P2ReactionFieldDipole.P0ReactionField - Class in etomica.potential: A 0-body potential that should be added along with this potential.
P2ReactionFieldDipoleTruncated - Class in etomica.potential
P2ReactionFieldDipoleTruncated(ISpace, IAtomPositionDefinition) - Constructor for class etomica.potential.P2ReactionFieldDipoleTruncated
P2ReactionFieldDipoleTruncated.P0ReactionField - Class in etomica.potential: A 0-body potential that should be added along with this potential.
P2RepRowley - Class in etomica.models.rowley: Purely repulsive potential from Rowley et al (2006) used for interactions between satellite sites, X.
P2RepRowley(ISpace) - Constructor for class etomica.models.rowley.P2RepRowley
P2RepRowley(ISpace, double, double) - Constructor for class etomica.models.rowley.P2RepRowley
P2RoughSphere - Class in etomica.potential: Basic hard-(rod/disk/sphere) potential, with surface roughness to couple rotation and translational motions.
P2RoughSphere(ISpace) - Constructor for class etomica.potential.P2RoughSphere
P2RoughSphere(ISpace, double, boolean) - Constructor for class etomica.potential.P2RoughSphere
p2S - Variable in class etomica.modules.sam.Sam
p2SCH2 - Variable in class etomica.modules.sam.Sam
p2SCH2t - Variable in class etomica.modules.sam.Sam
P2SemiclassicalAtomic - Class in etomica.potential: Effective semiclassical molecular potential using the approach of Takahashi and Imada http://dx.doi.org/10.1143/JPSJ.53.3765 as described by Schenter http://dx.doi.org/10.1063/1.1505441
P2SemiclassicalAtomic(ISpace, IPotentialTorque, double) - Constructor for class etomica.potential.P2SemiclassicalAtomic
P2SemiclassicalAtomic.AtomInfo - Interface in etomica.potential
P2SemiclassicalMolecular - Class in etomica.potential: Effective semiclassical molecular potential using the approach of Takahashi and Imada http://dx.doi.org/10.1143/JPSJ.53.3765 as described by Schenter http://dx.doi.org/10.1063/1.1505441
P2SemiclassicalMolecular(ISpace, IPotentialMolecularTorque) - Constructor for class etomica.potential.P2SemiclassicalMolecular
P2SemiclassicalMolecular.MoleculeInfo - Interface in etomica.potential
P2SemiclassicalMolecular.MoleculeInfoBrute - Class in etomica.potential
p2Soft - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
p2Soft - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
p2Soft - Variable in class etomica.potential.Potential2SoftSphericalLS
P2SoftSphere - Class in etomica.potential: Soft-sphere interatomic potential.
P2SoftSphere(ISpace) - Constructor for class etomica.potential.P2SoftSphere
P2SoftSphere(ISpace, double, double, int) - Constructor for class etomica.potential.P2SoftSphere
P2SoftSphericalTruncated - Class in etomica.potential: Wraps a soft-spherical potential to apply a truncation to it.
P2SoftSphericalTruncated(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncated
P2SoftSphericalTruncated.P0Lrc - Class in etomica.potential: Inner class that implements the long-range correction for this truncation scheme.
P2SoftSphericalTruncatedForceShifted - Class in etomica.potential: Soft-spherical potential class that shifts both the potential energy and the force such that both are 0 at the cutoff.
P2SoftSphericalTruncatedForceShifted(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedForceShifted
P2SoftSphericalTruncatedShifted - Class in etomica.potential: Wraps a soft-spherical potential to apply a truncation to it.
P2SoftSphericalTruncatedShifted(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedShifted
P2SoftSphericalTruncatedSwitched - Class in etomica.potential: Wraps a soft-spherical potential to apply a truncation to it.
P2SoftSphericalTruncatedSwitched(ISpace, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedSwitched
P2SoftTruncated - Class in etomica.potential: Wraps a soft-spherical potential to apply a truncation to it.
P2SoftTruncated(Potential2Soft, double, ISpace) - Constructor for class etomica.potential.P2SoftTruncated
P2SpheroPolyhedron - Class in etomica.potential
P2SpheroPolyhedron(ISpace) - Constructor for class etomica.potential.P2SpheroPolyhedron
P2Spin - Class in etomica.spin: Magnetic spin potential, with an energy defined by U = -J r1 dot r2 where J is a coupling parameter, and r1 and r2 are the vectors given by atom.coord.position.
P2Spin(ISpace) - Constructor for class etomica.spin.P2Spin
P2Spin(ISpace, double) - Constructor for class etomica.spin.P2Spin
P2SquareWell - Class in etomica.potential: Basic square-well potential.
P2SquareWell(ISpace) - Constructor for class etomica.potential.P2SquareWell
P2SquareWell(ISpace, double, double, double, boolean) - Constructor for class etomica.potential.P2SquareWell
P2SquareWellBonded - Class in etomica.modules.chainequilibrium: Similar to square-well potential, but considers and alters bonding states with collisions.
P2SquareWellBonded(ISpace, AtomLeafAgentManager, double, double, double) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded
P2SquareWellBonded - Class in etomica.modules.reactionequilibrium: Similar to square-well potential, but considers and alters bonding states with collisions.
P2SquareWellBonded(ISpace, AtomLeafAgentManager, double, double, double, boolean) - Constructor for class etomica.modules.reactionequilibrium.P2SquareWellBonded
P2SquareWellBonded.RingResult - Class in etomica.modules.chainequilibrium
P2SquareWellBonding - Class in etomica.modules.catalysis: Basic square-well potential.
P2SquareWellBonding(ISpace, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBonding
P2SquareWellBondingCO - Class in etomica.modules.catalysis: Basic square-well potential.
P2SquareWellBondingCO(ISpace, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBondingCO
P2SquareWellMonomer - Class in etomica.modules.colloid
P2SquareWellMonomer(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P2SquareWellMonomer
P2SquareWellOneSide - Class in etomica.modules.mu: Basic square-well potential.
P2SquareWellOneSide(ISpace) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
P2SquareWellOneSide(ISpace, double, double, double, boolean) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
P2SquareWellRadical - Class in etomica.modules.chainequilibrium: Similar to square-well potential, but considers and alters bonding states with collisions based on free radical reactions.
P2SquareWellRadical(ISpace, AtomLeafAgentManager, double, double, double, IRandom) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellRadical
P2SquareWellRobust - Class in etomica.potential: Basic square-well potential.
P2SquareWellRobust(ISpace) - Constructor for class etomica.potential.P2SquareWellRobust
P2SquareWellRobust(ISpace, double, double, double, boolean) - Constructor for class etomica.potential.P2SquareWellRobust
P2SquareWellSurface - Class in etomica.modules.catalysis: Basic square-well potential.
P2SquareWellSurface(ISpace, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
P2SquareWellSurface(ISpace, AtomLeafAgentManager, double, double, double, int) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
p2St - Variable in class etomica.modules.sam.Sam
p2SulfurSurfaceLJ - Variable in class etomica.modules.sam.Sam
p2SurfaceBond - Variable in class etomica.modules.sam.Sam
p2Tail - Variable in class etomica.modules.interfacial.InterfacialSW
p2TailTail - Variable in class etomica.modules.interfacial.InterfacialSW
P2Tether - Class in etomica.potential: Potential that acts like a hard string connecting the centers of two atoms.
P2Tether(ISpace) - Constructor for class etomica.potential.P2Tether
P2Tether(ISpace, double, boolean) - Constructor for class etomica.potential.P2Tether
P2TriangleWell - Class in etomica.potential: Hard core with an attractive tail that goes to zero linearly with r.
P2TriangleWell(ISpace) - Constructor for class etomica.potential.P2TriangleWell
P2TriangleWell(ISpace, double, double, double) - Constructor for class etomica.potential.P2TriangleWell
p2Truncated - Variable in class etomica.mappedvirial.MappedVirialLJ
p2Truncated - Variable in class etomica.mappedvirial.MappedVirialLJVGr
p2Truncated - Variable in class etomica.modules.vle.VLESim
p2TruncatedShifted - Variable in class etomica.mappedvirial.MappedU
P2Water3P - Class in etomica.models.water: 3-point potential for water.
P2Water3P(ISpace, double, double, double, double) - Constructor for class etomica.models.water.P2Water3P
P2Water3PSoft - Class in etomica.models.water: 3-point potential for water that can calculate gradient and torque (for the center of mass of the water molecule).
P2Water3PSoft(ISpace, double, double, double, double) - Constructor for class etomica.models.water.P2Water3PSoft
P2Water4P - Class in etomica.models.water: 4-point potential for water.
P2Water4P(ISpace, double, double, double, double, IAtomPositionDefinition) - Constructor for class etomica.models.water.P2Water4P
P2Water4PSoft - Class in etomica.models.water: 3-point potential for water that can calculate gradient and torque (for the center of mass of the water molecule).
P2Water4PSoft(ISpace, double, double, double, double, IAtomPositionDefinition) - Constructor for class etomica.models.water.P2Water4PSoft
P2Water4PSoft.AtomicTensorAtomicPair - Interface in etomica.models.water
P2WaterPotentialsJankowski - Class in etomica.potential
P2WaterPotentialsJankowski(ISpace, int, int, double, IPotentialAtomic) - Constructor for class etomica.potential.P2WaterPotentialsJankowski
P2WaterSPC - Class in etomica.models.water: SPC potential for water.
P2WaterSPC(ISpace) - Constructor for class etomica.models.water.P2WaterSPC
P2WaterSPCE - Class in etomica.models.water: SPC/E potential for water.
P2WaterSPCE(ISpace) - Constructor for class etomica.models.water.P2WaterSPCE
P2WaterSPCSoft - Class in etomica.models.water: SPC potential for water.
P2WaterSPCSoft(ISpace) - Constructor for class etomica.models.water.P2WaterSPCSoft
P2WaterSzalewicz - Class in etomica.models.water: Water potential as described by http://dx.doi.org/10.1063/1.4875097 This class handles 2-body, 3-body and induction terms.
P2WaterSzalewicz(ISpace, int) - Constructor for class etomica.models.water.P2WaterSzalewicz
P2WaterSzalewicz.Component - Enum in etomica.models.water
P2WaterSzalewicz.P2H2OSC - Class in etomica.models.water
P2WaterTIP4P - Class in etomica.models.water: TIP4P potential for water.
P2WaterTIP4P(ISpace) - Constructor for class etomica.models.water.P2WaterTIP4P
P2WaterTIP4P(ISpace, double) - Constructor for class etomica.models.water.P2WaterTIP4P
P2WaterTIP4PHardCore - Class in etomica.models.water: 4-point potential for water.
P2WaterTIP4PHardCore(ISpace, double, double, double, double, double) - Constructor for class etomica.models.water.P2WaterTIP4PHardCore
P2WaterTIP4PSoft - Class in etomica.models.water: TIP4P potential for water.
P2WaterTIP4PSoft(ISpace, double, IAtomPositionDefinition) - Constructor for class etomica.models.water.P2WaterTIP4PSoft
P2WCA - Class in etomica.potential: Weeks-Chandler-Andersen potential.
P2WCA(ISpace) - Constructor for class etomica.potential.P2WCA: Constructs potential using default sigma and epsilon given by Default class.
P2WCA(ISpace, double, double) - Constructor for class etomica.potential.P2WCA
P2XOrder - Class in etomica.normalmode: Hard potential that enforces ordering of the x-coordinates of the pairs.
P2XOrder(ISpace, Potential2HardSpherical) - Constructor for class etomica.normalmode.P2XOrder
P2Yukawa - Class in etomica.yukawa: Yukawa interatomic potential.
P2Yukawa(ISpace) - Constructor for class etomica.yukawa.P2Yukawa
P2Yukawa(ISpace, double, double) - Constructor for class etomica.yukawa.P2Yukawa
p3 - Variable in class etomica.virial.MayerFunctionMolecularThreeBody
p3 - Variable in class etomica.virial.MayerFunctionSphericalThreeBody
P3AdditiveQChem - Class in etomica.potential
P3AdditiveQChem() - Constructor for class etomica.potential.P3AdditiveQChem
P3AdditiveQChem.DampingParams - Class in etomica.potential
P3AxilrodTeller - Class in etomica.potential: Axilrod-Teller potential.
P3AxilrodTeller(ISpace, AtomTypeAgentManager) - Constructor for class etomica.potential.P3AxilrodTeller
P3AxilrodTeller.MyAgent - Class in etomica.potential
p3Bond - Variable in class etomica.modules.sam.Sam
P3BondAngle - Class in etomica.potential: Simple 3-body soft bond-angle potential
P3BondAngle(ISpace) - Constructor for class etomica.potential.P3BondAngle
P3BondAngleDreiding - Class in etomica.potential: Simple 3-body soft bond-angle for Dreiding potential * U(theta) = gamma * [ cos(theta) - cos(theta_e)]^2 where gamma is the potential's energy parameter theta_e is the equilibrium bond angle
P3BondAngleDreiding(ISpace, double, double) - Constructor for class etomica.potential.P3BondAngleDreiding
P3CPSNonAdditiveHe - Class in etomica.potential: Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHe(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHe
P3CPSNonAdditiveHeLessSimplified - Class in etomica.potential: Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHeLessSimplified(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHeLessSimplified
P3CPSNonAdditiveHeOrig - Class in etomica.potential: Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHeOrig(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHeOrig
P3CPSNonAdditiveHeSimplified - Class in etomica.potential: Simplified version of ab initio, non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
P3CPSNonAdditiveHeSimplified(ISpace) - Constructor for class etomica.potential.P3CPSNonAdditiveHeSimplified
P3GCPMAxilrodTeller(ISpace) - Constructor for class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
P3GCPMAxilrodTeller(ISpace) - Constructor for class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
P3HydrogenATM - Class in etomica.potential
P3HydrogenATM(ISpace) - Constructor for class etomica.potential.P3HydrogenATM
P3HydrogenATM.P3HydrogenAtomic - Class in etomica.potential
P3HydrogenAtomic(ISpace) - Constructor for class etomica.potential.P3HydrogenATM.P3HydrogenAtomic
P3HydrogenGarberoglioMolecular - Class in etomica.potential
P3HydrogenGarberoglioMolecular(ISpace) - Constructor for class etomica.potential.P3HydrogenGarberoglioMolecular
P3HydrogenManzhos - Class in etomica.potential
P3HydrogenManzhos(ISpace) - Constructor for class etomica.potential.P3HydrogenManzhos
P3HydrogenManzhos.P3HydrogenManzhosMolecular - Class in etomica.potential
P3HydrogenManzhosMolecular(ISpace) - Constructor for class etomica.potential.P3HydrogenManzhos.P3HydrogenManzhosMolecular
P3Induction - Class in etomica.potential: 3-body induction potential based on form used by Oakley and Wheatley.
P3Induction(ISpace, AtomTypeAgentManager) - Constructor for class etomica.potential.P3Induction
P3Induction.MyAgent - Class in etomica.potential
p3N2HellmannA - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
p3N2HellmannA - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
P3NitrogenHellmannNonAdditive - Class in etomica.potential
P3NitrogenHellmannNonAdditive(ISpace) - Constructor for class etomica.potential.P3NitrogenHellmannNonAdditive
p3ParametersFile - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
P3QChem - Class in etomica.potential
P3QChem() - Constructor for class etomica.potential.P3QChem
P3QChem.DampingParams - Class in etomica.potential
p4BondCCCC - Variable in class etomica.modules.sam.Sam
p4BondCCCS - Variable in class etomica.modules.sam.Sam
P4BondTorsion - Class in etomica.potential: Torsion potential.
P4BondTorsion(ISpace, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsion
P4BondTorsionAlkaneXCCH - Class in etomica.potential: slight modification from P4BondTorsion class(change energyAtAngle method) Siepmann's Alkane TraPPE-EH model, XCCH torsion potential, X can be H or C, H is for H on CH3 only U(torsion) = Cx * (1 -cos(3phi)); C(C):854K, C(H):717K
P4BondTorsionAlkaneXCCH(ISpace, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsionAlkaneXCCH
P4BondTorsionOPLS - Class in etomica.potential: OPLS Torsion potential.
P4BondTorsionOPLS(ISpace, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsionOPLS
P4TorsionDreiding - Class in etomica.potential: Simple 4-body soft bond-angle for Dreiding potential U(phi) = (1/2) * Vjk * {1 - cos [njk (phi - phiEq)]} where Vjk is the rotation barrier (always +ve) [unit Kelvin] njk is the periodicity (an integer) phiEq is the equilibrium dihedral angle [unit radians]
P4TorsionDreiding(ISpace, double, double, int) - Constructor for class etomica.potential.P4TorsionDreiding
pac - Variable in class etomica.util.numerical.AkimaSplineSmoother
PadeApproximation - Class in etomica.util.numerical: Class to approximate a power series with rational function (Pade Approximation) Pade[K/L] = A_K/ C_L = B_M with Kth, Lth and Mth order, where K + L = M a0 + a1*x + a2*x^2 + ...
PadeApproximation(double[], int, int) - Constructor for class etomica.util.numerical.PadeApproximation
PadeApproximation.VirialParam - Class in etomica.util.numerical
paint(Graphics) - Method in class etomica.graphics.AboutBoxWindow
paint(Graphics) - Method in class etomica.graphics.DisplayCanvas
paint(Graphics) - Method in class etomica.graphics.DisplayScrollingGraph
paint() - Method in class etomica.modules.clustergenerator.ClusterPanel
paint() - Method in class etomica.modules.clustergenerator.Plot: Classes which inherit from Plot must define this method.
paint(Graphics) - Method in class etomica.modules.clustergenerator.Plot
paint(Graphics) - Method in class etomica.util.Grabber.ImagePanel
paintComponent(Graphics) - Method in class etomica.graphics.EtomicaPlot
pair - Variable in class etomica.association.BiasVolume2SiteAceticAcid
pair - Variable in class etomica.association.BiasVolumeAceticAcid
pair - Variable in class etomica.atom.iterator.ANIntergroupExchange
pair - Variable in class etomica.atom.iterator.ApiIndexList
pair - Variable in class etomica.atom.iterator.ApiInnerVariable
pair - Variable in class etomica.atom.iterator.ApiIntergroup
pair - Variable in class etomica.atom.iterator.MpiInnerVariable
pair - Variable in class etomica.mappedvirial.MappedUpotential
pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
pair - Variable in class etomica.models.co2.PNCO2GCPM
pair - Variable in class etomica.models.co2.PNGCPM
pair - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
pair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
pair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
pair - Variable in class etomica.models.water.PNWaterGCPM
pair - Variable in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
pair - Variable in class etomica.nbr.list.NeighborListManagerSlanty
pair - Variable in class etomica.normalmode.MCMoveAtomCoupled
pair - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
pair - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
pair - Variable in class etomica.normalmode.MCMoveAtomSuperBox
pair - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
pair - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
pair - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
pairAB - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
pairAB - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
pairAB - Variable in class etomica.normalmode.MCMoveAtomSuperBox
pairAgents - Variable in class etomica.models.co2.PNGCPM
pairDone - Variable in class etomica.virial.PotentialCommonAtomic
pairDone - Variable in class etomica.virial.PotentialGroupPI
pairForce(IAtom, IAtom) - Method in class etomica.models.water.P2Water4PSoft
pairId(int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams: Returns the pair ID for the given indices (id0, id1, id2)
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
pairMatrix - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
pairOnly - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
pairOnly - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
pairOnly - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
pairOnly - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
pairOnly - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
pairOnly - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
pairOnly - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
pairOnly - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
pairOnly - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
pairPolarization - Variable in class etomica.models.co2.PNGCPM
pairPotential - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
pairPotential - Variable in class etomica.normalmode.MCMoveAtomCoupled
pairPotential - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
pairPotentialIndex - Variable in class etomica.normalmode.MCMoveAtomCoupled
pairSum - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
PALETTE_ALTLOC - Static variable in class org.jmol.constant.StaticConstants
PALETTE_AMINO - Static variable in class org.jmol.constant.StaticConstants
PALETTE_CHAIN - Static variable in class org.jmol.constant.StaticConstants
PALETTE_CPK - Static variable in class org.jmol.constant.StaticConstants
PALETTE_ENERGY - Static variable in class org.jmol.constant.StaticConstants
PALETTE_FIXEDTEMP - Static variable in class org.jmol.constant.StaticConstants
PALETTE_FORMAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_GROUP - Static variable in class org.jmol.constant.StaticConstants
PALETTE_INSERTION - Static variable in class org.jmol.constant.StaticConstants
PALETTE_JMOL - Static variable in class org.jmol.constant.StaticConstants
PALETTE_MOLECULE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_MONOMER - Static variable in class org.jmol.constant.StaticConstants
PALETTE_NONE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_PARTIAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_POLYMER - Static variable in class org.jmol.constant.StaticConstants
PALETTE_PROPERTY - Static variable in class org.jmol.constant.StaticConstants
PALETTE_RASMOL - Static variable in class org.jmol.constant.StaticConstants
PALETTE_SHAPELY - Static variable in class org.jmol.constant.StaticConstants
PALETTE_STRAIGHTNESS - Static variable in class org.jmol.constant.StaticConstants
PALETTE_STRUCTURE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_SURFACE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_TEMP - Static variable in class org.jmol.constant.StaticConstants
PALETTE_TYPE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_VARIABLE - Static variable in class org.jmol.constant.StaticConstants
PALETTE_VOLATILE - Static variable in class org.jmol.constant.StaticConstants
panel - Variable in class etomica.graphics.DeviceBox: Displayed panel that holds the label and value (not yet used; meant to implement to make lightweight display)
panel - Variable in class etomica.graphics.DisplayPlot
panel - Variable in class etomica.graphics.DisplayTable
panel - Variable in class etomica.graphics.DisplayTextBox: Displayed panel that holds the label and value (not yet used; meant to implement to make lightweight display)
panel - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
panel - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
PanelMainFrame - Class in etomica.virial.GUI.containers
PanelMainFrame(int, int) - Constructor for class etomica.virial.GUI.containers.PanelMainFrame
panelParentGroup - Variable in class etomica.graphics.DisplayTextBoxesCAE
parab - Static variable in class etomica.potential.P2WaterPotentialsJankowski
Parallelepiped - Class in etomica.math.geometry: A polyhedron composed of three pairs of rectangular faces placed opposite each other and joined at arbitrary angles.
Parallelepiped(ISpace) - Constructor for class etomica.math.geometry.Parallelepiped: Default constructor makes a cube of unit size
Parallelepiped(ISpace, IVector, IVector, IVector) - Constructor for class etomica.math.geometry.Parallelepiped: Constructs a parallelepiped with the given edge vectors.
Parallelogram - Class in etomica.math.geometry: A quadrilateral with opposite sides parallel .
Parallelogram(ISpace) - Constructor for class etomica.math.geometry.Parallelogram: Default constructor makes a square of unit size
Parallelogram(ISpace, IVector, IVector) - Constructor for class etomica.math.geometry.Parallelogram: Constructs a parallelogram with the given edge vectors.
Parallelotope - Interface in etomica.math.geometry: Polytope having parallel faces, and which can be specified via a set of edge vectors.
Param() - Constructor for class etomica.AlkaneEH.CH4NVT.Param
Param() - Constructor for class etomica.AlkaneEH.DHS_NVT.Param
Param() - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site.Param
Param() - Constructor for class etomica.dielectric.DHS_NVT.Param
Param() - Constructor for class etomica.dielectric.DLJ_NVT_1site.Param
Param() - Constructor for class etomica.dielectric.TIP4P_NVT.Param
param - Variable in class etomica.modules.interfacial.FitTanh
param - Static variable in class etomica.potential.P2WaterPotentialsJankowski
param - Variable in class etomica.surfacetension.FitTanh
PARAM_ALL - Static variable in class etomica.graph.operations.MaxIsomorph: Parameters instance which does not filter out any graph property.
PARAM_ROOTY - Static variable in class etomica.graph.operations.MaxIsomorph
ParameterBase - Class in etomica.util: Base class for all parameter wrapper implementations.
ParameterBase() - Constructor for class etomica.util.ParameterBase
parameterGraphic() - Method in class etomica.graphics.DevicePlotPoints: Returns the panel that contains the parameter sliders.
ParameterParser - Interface in etomica.util
Parameters - Interface in etomica.graph.operations
parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
parametersB - Variable in class etomica.potential.P2NitrogenHellmann
parametersB - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
ParameterSetMEAM - Class in etomica.meam: This class provides the MEAM parameters for the SAC alloy constituents (Ag, Cu, and Sn) and for the reference structures required for cross potentials (the pair potentials between atoms of different types).
ParameterSetMEAM(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.meam.ParameterSetMEAM
params - Variable in class etomica.graph.operations.UnaryChain.ChainParameters
Params() - Constructor for class etomica.meam.EFSTungsten.Params
params - Static variable in class etomica.models.water.P2WaterSzalewicz
Params() - Constructor for class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
params - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
params - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
params3 - Static variable in class etomica.models.water.P2WaterSzalewicz
paramsManager - Variable in class etomica.potential.P3AxilrodTeller
paramsManager - Variable in class etomica.potential.P3Induction
parent - Variable in class etomica.atom.Atom
parentColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
parentGroup - Variable in class etomica.atom.iterator.ApiIndexList
parentType - Variable in class etomica.atom.AtomTypeLeaf
ParmedParser - Class in etomica.parser: Class that generates ParmedStructure objects by invoking the ParmEd library and serializing its Structure object using JSON.
ParmedParser() - Constructor for class etomica.parser.ParmedParser
ParmedStructure - Class in etomica.parser: Class that contains the data from a ParmEd Structure, and has methods to load this data into various etomica components.
parse(String) - Method in class etomica.graph.engine.impl.ParserImpl
parse(String) - Method in interface etomica.graph.engine.Parser
parse(String, ParsePosition) - Method in class etomica.util.ScientificFormat: Parse out a number from the given text and return it as a Long if possible; otherwise, return it as a Double.
parseARGB(String) - Method in class etomica.graph.view.rasterizer.Main.ColorOptionHandler: Parse the input value, which should be in the following format: a.r.g.b where a, r, g and b are integer values, in decimal notation, between 0 and 255.
ParseArgs - Class in etomica.util: Class that handles parsing of commandline arguments.
ParseArgs() - Constructor for class etomica.util.ParseArgs
ParseArgs(ParameterBase) - Constructor for class etomica.util.ParseArgs
parseArgs(String[]) - Method in class etomica.util.ParseArgs: Parses each argument and attempts to match it with a field from parameterWrapper and sets the field to the value from the next argument.
parseArgs(String[], boolean) - Method in class etomica.util.ParseArgs
parseAsDecimal(String, ParsePosition) - Method in class etomica.util.ScientificFormat: parse the input string, interpreting it as regular decimal format.
parseAsExponential(String, ParsePosition) - Method in class etomica.util.ScientificFormat: parse the input string, interpreting it as exponential format.
parseAsFlexible(String, ParsePosition) - Method in class etomica.util.ScientificFormat: parse the input string, interpreting it as either regular decimal format or exponential format.
parseFloatArray(String) - Static method in class org.jmol.util.Parser
parseFloatArray2d(String) - Static method in class org.jmol.util.Parser
parseFloatArray3d(String) - Static method in class org.jmol.util.Parser
parseFloatArrayBsData(String[], BitSet, float[]) - Static method in class org.jmol.util.Parser
parseFloatArrayData(String[], float[]) - Static method in class org.jmol.util.Parser: parses a string array for floats.
parseFloatArrayDataN(String[], float[], int) - Static method in class org.jmol.util.Parser: parses a string array for floats.
parseFloatArrayFromMatchAndField(String, BitSet, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser: the major lifter here.
parseFloatArrayNext(String, int[]) - Static method in class org.jmol.util.Parser
parseFloatNext(String, int[]) - Static method in class org.jmol.util.Parser
parseFloatRange(String, int, int[]) - Static method in class org.jmol.util.Parser
parseFloatStr(String) - Static method in class org.jmol.util.Parser
parseFloatStrict(String) - Static method in class org.jmol.util.Parser
parseGromacs(File, File) - Static method in class etomica.parser.ParmedParser: Parses the given Gromacs .top and .gro files using the ParmEd python library.
parseGromacsResourceFiles(String, String) - Static method in class etomica.parser.ParmedParser: Convenience method to parse gromacs files located in the etomica-core/src/main/resources directory.
parseInt(String) - Static method in class org.jmol.util.Parser
parseIntNext(String, int[]) - Static method in class org.jmol.util.Parser
parseIntRadix(String, int) - Static method in class org.jmol.util.Parser
parseIntRange(String, int, int[]) - Static method in class org.jmol.util.Parser
ParseObj - Class in etomica.modules.render
ParseObj(String) - Constructor for class etomica.modules.render.ParseObj
ParseObj.BondInfo - Class in etomica.modules.render
Parser - Interface in etomica.graph.engine
parser - Variable in class etomica.modules.render.RenderMD
Parser - Class in org.jmol.util
Parser() - Constructor for class org.jmol.util.Parser
Parser.Assignment - Interface in etomica.graph.engine
Parser.BinaryOp - Interface in etomica.graph.engine
Parser.BinaryOpByte - Interface in etomica.graph.engine
Parser.Command - Interface in etomica.graph.engine
Parser.CommandPropertyValue - Interface in etomica.graph.engine
Parser.CommandValue - Interface in etomica.graph.engine
Parser.CommandVariable - Interface in etomica.graph.engine
Parser.CommandVariableValue - Interface in etomica.graph.engine
Parser.Constructor - Interface in etomica.graph.engine
Parser.ConstructorColored - Interface in etomica.graph.engine
Parser.ConstructorMono - Interface in etomica.graph.engine
Parser.Expression - Interface in etomica.graph.engine
Parser.ParserException - Exception in etomica.graph.engine
Parser.Property - Interface in etomica.graph.engine
Parser.Statement - Interface in etomica.graph.engine
Parser.StrictExpression - Interface in etomica.graph.engine
Parser.UnaryOp - Interface in etomica.graph.engine
Parser.UnaryOpByte - Interface in etomica.graph.engine
Parser.UnaryOpByteMap - Interface in etomica.graph.engine
Parser.UnaryOpColor - Interface in etomica.graph.engine
Parser.UnaryOpThreeColor - Interface in etomica.graph.engine
Parser.UnaryOpTwoByte - Interface in etomica.graph.engine
Parser.Value - Interface in etomica.graph.engine
Parser.Variable - Interface in etomica.graph.engine
parseRect(String) - Method in class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
ParserException(String) - Constructor for exception etomica.graph.engine.Parser.ParserException
ParserException(String, Throwable) - Constructor for exception etomica.graph.engine.Parser.ParserException
ParserImpl - Class in etomica.graph.engine.impl
ParserImpl() - Constructor for class etomica.graph.engine.impl.ParserImpl
ParserLAMMPS - Class in etomica.parser
ParserLAMMPS() - Constructor for class etomica.parser.ParserLAMMPS
ParserLAMMPS.Options - Class in etomica.parser
ParserLAMMPS.Stuff - Class in etomica.parser
ParserLAMMPS.Truncation - Enum in etomica.parser
parsers - Variable in class etomica.util.ParameterBase
parseStringInfestedFloatArray(String, BitSet, float[]) - Static method in class org.jmol.util.Parser: parses a "dirty" string for floats.
parseToken(String) - Static method in class org.jmol.util.Parser
parseTokenNext(String, int[]) - Static method in class org.jmol.util.Parser
parseTokenRange(String, int, int[]) - Static method in class org.jmol.util.Parser
parseTrimmed(String) - Static method in class org.jmol.util.Parser
parseTrimmedAt(String, int) - Static method in class org.jmol.util.Parser
parseTrimmedRange(String, int, int) - Static method in class org.jmol.util.Parser
PARTIAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
PARTIAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
partialcharge - Static variable in class org.jmol.script.Token
partialdots - Static variable in class org.jmol.script.Token
particleCounters - Variable in class etomica.atom.iterator.ANIntragroupExchange
particles - Variable in class etomica.atom.iterator.ANIntragroupExchange
PartitionedIterator - Class in etomica.graph.iterators
PartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) - Constructor for class etomica.graph.iterators.PartitionedIterator
partitions - Variable in class etomica.virial.ClusterSinglyConnected
partitionsA - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
partitionsC - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
PartitionsP - Class in etomica.veos.bigdecimal: Number of partitions.
PartitionsP() - Constructor for class etomica.veos.bigdecimal.PartitionsP: Default constructor initializing a list of partitions up to 7.
partnerColor - Variable in class etomica.graphics.ColorSchemeColliders: Color applied to the upList atom of the colliding pair
partners - Variable in class etomica.atom.iterator.ApiIndexList
pascal() - Static method in class etomica.math.SpecialFunctions
pascal() - Static method in class etomica.potential.P2O2Bartolomei
Pascal - Class in etomica.units: The Pascal unit of pressure, equal to 1 N/m^2.
path - Static variable in class org.jmol.script.Token
pathforallfiles - Static variable in class org.jmol.script.Token
pause() - Method in class etomica.action.activity.ActivityGroupParallel
pause() - Method in class etomica.action.activity.ActivityGroupSeries: Requests a pause in the performance of the actions.
pause() - Method in class etomica.action.Activity: Requests that the Activity pause its execution.
pause - Static variable in class org.jmol.script.Token
pauseAfterEachAction - Variable in class etomica.action.activity.ActivityGroupSeries
pauseRequested - Variable in class etomica.action.Activity
pbuf - Variable in class org.jmol.g3d.Graphics3D
pbufT - Variable in class org.jmol.g3d.Graphics3D
pBW - Variable in class etomica.interfacial.LJMC
pBW - Variable in class etomica.interfacial.LJMD
pc - Variable in class etomica.data.meter.MeterPressureTensor
pc - Variable in class etomica.data.meter.MeterRDFPC
pc - Variable in class etomica.freeenergy.npath.DataSourceEnergies
pc - Variable in class etomica.interfacial.MeterWallForce
pc - Variable in class etomica.liquidLJ.MeterPUCut
pc - Variable in class etomica.liquidLJ.MeterPUCutLS
pc - Variable in class etomica.mappedvirial.MeterMappedU
pc - Variable in class etomica.mappedvirial.MeterMappedVirial
pc - Variable in class etomica.mappedvirial.MeterMappedVirialV
pc - Variable in class etomica.modules.materialfracture.MaterialFracture
pc - Variable in class etomica.modules.materialfracture.MeterLoad
pc - Variable in class etomica.modules.materialfracture.MeterStress
pc - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
pc - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
pc - Variable in class etomica.modules.sam.MeterWallPressure
pc - Variable in class etomica.threaded.atom.PotentialMasterListWorker
pc - Variable in class etomica.threaded.domain.PotentialMasterListWorker
pc - Variable in class etomica.threaded.PotentialCalculationForceSumThreaded
pCalc(int, double[], double) - Method in class etomica.veos.QSeries: Computes the pressure via dlnQ/dV based on the volume series for Q given by coeffQ.
pCalc(double, double) - Method in class etomica.veos.Ushcats
pcDADv2 - Variable in class etomica.liquidLJ.MeterPUCut
pcDADv2 - Variable in class etomica.liquidLJ.MeterPUCutLS
pCenter - Variable in class etomica.normalmode.MeterDDP
pCenter - Variable in class etomica.normalmode.MeterDP
pcForce - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
pcForce - Variable in class etomica.mappedvirial.MeterMappedU
pcForce - Variable in class etomica.mappedvirial.MeterMappedVirial
pcForce - Variable in class etomica.mappedvirial.MeterMappedVirialV
pcForce - Variable in class etomica.mappedvirial.MeterMeanForce
pcForce - Variable in class etomica.surfacetension.SurfaceTensionMapped
pcForceSum - Variable in class etomica.normalmode.MeterDADB
pcForceSum - Variable in class etomica.normalmode.MeterSolidPropsLJ
pcGB - Variable in class etomica.dimer.SimDimerMEAMGB
pcom - Variable in class etomica.util.numerical.Function1d
PCopy - Class in etomica.graph.operations
PCopy() - Constructor for class etomica.graph.operations.PCopy
pCross - Variable in class etomica.normalmode.HSNPT
pdbaddhydrogens - Static variable in class org.jmol.script.Token
pdbgetheader - Static variable in class org.jmol.script.Token
pdbsequential - Static variable in class org.jmol.script.Token
PDBWriter - Class in etomica.action: Action that dumps a box's configuration to an PDB file.
PDBWriter() - Constructor for class etomica.action.PDBWriter
PDBWriter(IBox) - Constructor for class etomica.action.PDBWriter
PDF - Static variable in class etomica.graph.view.rasterizer.DestinationType
PDF_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
PDF_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
PDF_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
PE(IVector) - Method in interface etomica.api.IVectorMutable: Plus-equals (+=) operation.
PE(double) - Method in interface etomica.api.IVectorMutable: Plus-equals (+=) operation, causing a constant value to be added to all components of this vector.
PE(IData) - Method in interface etomica.data.IData: Plus-equals (+=) operation.
PE(double) - Method in interface etomica.data.IData: Plus-equals (+=) operation, adding given value to all values in data.
PE(IData) - Method in class etomica.data.types.DataDouble: Plus-equals (+=) operation.
PE(double) - Method in class etomica.data.types.DataDouble: Plus-equals (+=) operation.
PE(IData) - Method in class etomica.data.types.DataDoubleArray: Plus-equals (+=) operation.
PE(double) - Method in class etomica.data.types.DataDoubleArray: Plus-equals (+=) operation.
PE(IData) - Method in class etomica.data.types.DataDoubleBDArray: Plus-equals (+=) operation.
PE(double) - Method in class etomica.data.types.DataDoubleBDArray: Plus-equals (+=) operation.
PE(IData) - Method in class etomica.data.types.DataGroup
PE(double) - Method in class etomica.data.types.DataGroup
PE(IData) - Method in class etomica.data.types.DataTensor: Plus-equals (+=) operation.
PE(double) - Method in class etomica.data.types.DataTensor: Plus-equals (+=) operation.
PE(IData) - Method in class etomica.data.types.DataVector: Plus-equals (+=) operation.
PE(double) - Method in class etomica.data.types.DataVector: Plus-equals (+=) operation.
PE(Quaternion) - Method in class etomica.math.Quaternion: Adds the input Quaternion components to its components.
PE(double) - Method in interface etomica.space.Tensor
PE(Tensor) - Method in interface etomica.space.Tensor
PE(int, int, double) - Method in interface etomica.space.Tensor
PE(double) - Method in class etomica.space1d.Tensor1D
PE(int, int, double) - Method in class etomica.space1d.Tensor1D
PE(Tensor) - Method in class etomica.space1d.Tensor1D
PE(double) - Method in class etomica.space1d.Vector1D
PE(IVector) - Method in class etomica.space1d.Vector1D
PE(double) - Method in class etomica.space2d.Tensor2D
PE(Tensor) - Method in class etomica.space2d.Tensor2D
PE(int, int, double) - Method in class etomica.space2d.Tensor2D
PE(IVector) - Method in class etomica.space2d.Vector2D
PE(double) - Method in class etomica.space2d.Vector2D
PE(double) - Method in class etomica.space3d.Tensor3D
PE(Tensor) - Method in class etomica.space3d.Tensor3D
PE(int, int, double) - Method in class etomica.space3d.Tensor3D
PE(IVector) - Method in class etomica.space3d.Vector3D
PE(double) - Method in class etomica.space3d.Vector3D
PE(double) - Method in class etomica.spaceNd.TensorND
PE(Tensor) - Method in class etomica.spaceNd.TensorND
PE(int, int, double) - Method in class etomica.spaceNd.TensorND
PE(IVector) - Method in class etomica.spaceNd.VectorND
PE(double) - Method in class etomica.spaceNd.VectorND
PE(IBigValue) - Method in class etomica.veos.BigValue: Plus-equals (+=) operation.
PE(IBigValue) - Method in interface etomica.veos.IBigValue: Plus-equals (+=) operation.
PE(IBigValue) - Method in class etomica.veos.MyBigDecimal: Plus-equals (+=) operation.
PEa1Tt1(double, Tensor) - Method in interface etomica.space.Tensor
PEa1Tt1(double, Tensor) - Method in class etomica.space1d.Tensor1D
PEa1Tt1(double, Tensor) - Method in class etomica.space2d.Tensor2D
PEa1Tt1(double, Tensor) - Method in class etomica.space3d.Tensor3D
PEa1Tt1(double, Tensor) - Method in class etomica.spaceNd.TensorND
PEa1Tv1(double, IVector) - Method in interface etomica.api.IVectorMutable: Increments (+=) components by (a1 * v1)
PEa1Tv1(double, IVector) - Method in class etomica.space1d.Vector1D
PEa1Tv1(double, IVector) - Method in class etomica.space2d.Vector2D
PEa1Tv1(double, IVector) - Method in class etomica.space3d.Vector3D
PEa1Tv1(double, IVector) - Method in class etomica.spaceNd.VectorND
PEa1Tv1(double, IBigValue) - Method in class etomica.veos.BigValue: Plus-equals (+=) a1 times v1.
PEa1Tv1(double, IBigValue) - Method in interface etomica.veos.IBigValue: Plus-equals (+=) a1 times v1.
PEa1Tv1(double, IBigValue) - Method in class etomica.veos.MyBigDecimal: Plus-equals (+=) a1 times v1.
peek() - Method in class etomica.lattice.RectangularLattice.Iterator
peek() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Returns the next iterate without advancing the iterator.
peek() - Method in interface etomica.lattice.SiteIterator: Returns the next iterate without advancing the iterator.
PENDING - Static variable in class etomica.action.activity.Controller.ActionStatus
pendingActions - Variable in class etomica.action.activity.ActivityGroupSeries
Percent - Class in etomica.units: Decimal representation of something that represents the fractional amount of a whole (e.g., mole fraction) as a percentage value typically between 0 and 100.
percent - Static variable in class org.jmol.script.Token
percentvdwatom - Static variable in class org.jmol.script.Token
PercusYevick - Class in etomica.virial: Calculates the Percus-Yevick (PY) virial coefficients of second to Mth order for any spherically-symmetric Mayer function, fr.
PercusYevick() - Constructor for class etomica.virial.PercusYevick
PercusYevick1QC - Class in etomica.virial: Computes the Percus-Yevick compressibility-route approximation to the first quantum correction of Bn, where the first quantum correction is as defined Kim and Henderson (1968,1966).
PercusYevick1QC() - Constructor for class etomica.virial.PercusYevick1QC
periodicity - Variable in class etomica.nbr.cell.Api1ACell
periodicity - Variable in class etomica.nbr.cell.ApiAACell
periodicity - Variable in class etomica.nbr.cell.molecule.Mpi1ACell
periodicity - Variable in class etomica.nbr.cell.molecule.MpiAACell
periodicity - Variable in class etomica.nbr.site.Api1ASite
PermutationDegenerateIterator - Class in etomica.math.discrete: Iterator that returns unique permutations of an array of integers, with degeneracy such that some of the integers may appear more than once in the array.
PermutationDegenerateIterator(int) - Constructor for class etomica.math.discrete.PermutationDegenerateIterator: Constructs instance whose iterates are int[] of length n.
PermutationIterator - Class in etomica.math.discrete: Iterator that returns different permutations of a sequence of integers when called in successive iterations.
PermutationIterator(int) - Constructor for class etomica.math.discrete.PermutationIterator
PermutationIterator - Class in etomica.virial.cluster
PermutationIterator(int[]) - Constructor for class etomica.virial.cluster.PermutationIterator
permutations - Variable in class etomica.virial.ClusterBonds
Permutator - Interface in etomica.graph.model
perParticleFrequency - Variable in class etomica.integrator.mcmove.MCMoveBox: Flag indicating whether nominal frequency is interpreted as a perParticleFrequency, or as a full frequency.
perspective(int, float) - Method in class g3dsys.control.G3DSys: Handles perspective based on depth and diameter.
perspectivedepth - Static variable in class org.jmol.script.Token
perspectivemodel - Static variable in class org.jmol.script.Token
pEst - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
PETA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺¹⁵.
PEv1v2(IVector, IVector) - Method in interface etomica.space.Tensor: Increments this by the dyadic or outer product of the given vectors.
PEv1v2(IVector, IVector) - Method in class etomica.space1d.Tensor1D
PEv1v2(IVector, IVector) - Method in class etomica.space2d.Tensor2D
PEv1v2(IVector, IVector) - Method in class etomica.space3d.Tensor3D
PEv1v2(IVector, IVector) - Method in class etomica.spaceNd.TensorND
pFast - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
pFF - Variable in class etomica.interfacial.LJMC
pFF - Variable in class etomica.interfacial.LJMD
pFull - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
pHarmonic - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
pHarmonic - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
phaseAngles - Variable in class etomica.normalmode.NormalModesVariable
phi(int, double) - Static method in class etomica.densityofstate.CopyOfOrthogonalPolynomial
phi(int, double, double) - Static method in class etomica.densityofstate.OrthogonalPolynomial
PHI - Static variable in class etomica.meam.PotentialMEAM
phi - Static variable in class org.jmol.script.Token
phi2Sum - Variable in class etomica.normalmode.MeterTiltRotationStdev
phiData - Variable in class etomica.data.meter.MeterDihedralAngle
phiEq - Variable in class etomica.potential.P4TorsionDreiding
phiSlider - Variable in class etomica.modules.sam.SamGraphic
phiSum - Variable in class etomica.normalmode.MeterTiltRotationStdev
phongexponent - Static variable in class org.jmol.script.Token
phongExponent - Static variable in class org.jmol.util.Shader
pi - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
pi(MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Euler's constant.
pi(BigInteger) - Method in class etomica.veos.bigdecimal.Prime: return the count of primes <= n
picking - Static variable in class org.jmol.script.Token
pickingspinrate - Static variable in class org.jmol.script.Token
pickingstyle - Static variable in class org.jmol.script.Token
picklabel - Static variable in class org.jmol.script.Token
PICO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-12.
Picosecond - Class in etomica.units: Simulation unit of time.
pidOf(Object) - Static method in enum org.jmol.constant.EnumPalette
PINK - Static variable in class org.jmol.util.Colix
PistonCylinder - Class in etomica.modules.pistoncylinder: Simple hard-sphere MD in piston-cylinder apparatus
PistonCylinder(int) - Constructor for class etomica.modules.pistoncylinder.PistonCylinder
PistonCylinderGraphic - Class in etomica.modules.pistoncylinder
PistonCylinderGraphic(PistonCylinder, ISpace) - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic: Creates a PistonCylinder graphic instance.
PistonCylinderGraphic.Applet - Class in etomica.modules.pistoncylinder
PistonCylinderGraphic.ModifierAtomDiameter - Class in etomica.modules.pistoncylinder
PistonCylinderGraphic.ModifierPistonDensity - Class in etomica.modules.pistoncylinder
PistonPlane - Class in etomica.modules.pistoncylinder: Wrap a P1HardMovingBoundary and make it look like a Plane.
PistonPlane(ISpace, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.PistonPlane
pistonPotential - Variable in class etomica.modules.pistoncylinder.MeterRDFCylinder
pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonCylinder
pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonPlane
pistonUpdateRequested() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
pixel - Variable in class etomica.graphics.DisplayCanvas
Pixel - Class in etomica.units: Unit converting between simulation unit of length and pixels rendered in an image.
Pixel() - Constructor for class etomica.units.Pixel: Constructs with default of 10 pixels per Angstrom.
Pixel(double) - Constructor for class etomica.units.Pixel: Constructor for Pixel.
pixelUnitToMillimeter - Variable in class etomica.graph.view.rasterizer.SVGConverter: Millimeters Per Pixel
pixelX - Variable in class etomica.util.Grabber.CornerData
pixelY - Variable in class etomica.util.Grabber.CornerData
pj - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
pkl - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
pkl - Variable in class etomica.virial.MCMoveClusterRingRegrow
pkl - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
PLANCK_H - Static variable in class etomica.util.Constants: Planck's constant, in simulation units.
Plane - Class in etomica.math.geometry: Class describing a plane occupying a 3-dimensional space.
Plane(ISpace) - Constructor for class etomica.math.geometry.Plane: Default constructor returns the y-z plane.
Plane(Plane) - Constructor for class etomica.math.geometry.Plane: Constructs a new Plane as a copy of the given one.
Plane(ISpace, double, double, double, double) - Constructor for class etomica.math.geometry.Plane: Constructs a Plane satisfying the equation a x + b y + c z + d = 0
plane - Static variable in class org.jmol.script.Token
PLat - Variable in class etomica.normalmode.MeterSolidProps
PLat - Variable in class etomica.normalmode.MeterSolidPropsLJ
Platform - Class in org.jmol.awt
Platform() - Constructor for class org.jmol.awt.Platform
play - Static variable in class org.jmol.script.Token
playDumb - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
playrev - Static variable in class org.jmol.script.Token
plgndr(int, int, double) - Static method in class etomica.util.AssociatedPolynomial
plm(int, int, double) - Static method in class etomica.potential.P2O2Bartolomei
plmrb(double[][], double, int) - Method in class etomica.potential.P2HydrogenPatkowski
plmrb(double[][], double, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
plot - Variable in class etomica.graphics.DisplayPlot
plot - Variable in class etomica.meam.MEAM_3DMDwithGB
plot - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
plot - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
plot - Variable in class etomica.meam.MEAM_MC
plot - Variable in class etomica.meam.MEAMMd3D
Plot - Class in etomica.modules.clustergenerator: Used from comphys.graphic.plot A class which makes plotting a little more convenient than using Java's Graphics methods.
Plot() - Constructor for class etomica.modules.clustergenerator.Plot: Constructor sets default size of the plot
Plot(Color, int, int) - Constructor for class etomica.modules.clustergenerator.Plot
plot - Variable in class etomica.simulation.prototypes.LjMd2D
plot - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
plot - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
plot3d - Static variable in class org.jmol.script.Token
plotAction - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
PlotAction(int) - Constructor for class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
plotAction - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
PlotAction(int) - Constructor for class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
plotBox(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
plotD - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
plotImage(int, int, int, Object, Graphics3D, short, int, int) - Method in class org.jmol.g3d.Graphics3D
plotImage(int, int, int, Image, Graphics3D, short, int, int) - Method in class org.jmol.util.GData
plotImagePixel(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
plotLine(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
plotP - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
plotPanel - Variable in class etomica.graphics.SimulationPanel
plotPixelClippedP3i(Point3i) - Method in class org.jmol.g3d.Graphics3D
plotRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
plots - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
plotsPane - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
plotString(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
plotStringCenter(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
plotT - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
plotText(int, int, int, int, int, String, JmolFont, Graphics3D) - Method in class org.jmol.g3d.Graphics3D
plotText(int, int, int, int, int, String, JmolFont, Graphics3D) - Method in class org.jmol.util.GData
plus(Complex) - Method in class etomica.math.Complex: Addition of Complex numbers (doesn't change this Complex number).
plus(Matrix) - Method in class etomica.math.linearalgebra.Matrix
plus(Rational) - Method in class etomica.util.Rational: Returns a new Rational instance, which is the result of adding the given Rational to this Rational.
pmesh - Static variable in class org.jmol.script.Token
pmlt - Variable in class etomica.threaded.atom.PotentialMasterListWorker
pmlt - Variable in class etomica.threaded.domain.PotentialMasterListWorker
pN2HellmannA - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
pNA - Variable in class etomica.virial.MayerFunctionNonAdditiveFull
PNCO2GCPM - Class in etomica.models.co2: GCPM CO2 potential class (GCPCDO).
PNCO2GCPM(ISpace) - Constructor for class etomica.models.co2.PNCO2GCPM
PNCO2GCPM(ISpace, int) - Constructor for class etomica.models.co2.PNCO2GCPM
PNCO2GCPM.Component - Enum in etomica.models.co2
PNCO2GCPM.P3GCPMAxilrodTeller - Class in etomica.models.co2
PNG - Static variable in class etomica.graph.view.rasterizer.DestinationType
PNG_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
PNG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
PNG_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
PNGCPM - Class in etomica.models.co2: Generic GCPM potential class, capable of handling both CO2 and water.
PNGCPM(ISpace, AtomTypeAgentManager, int) - Constructor for class etomica.models.co2.PNGCPM
PNGCPM(ISpace, AtomTypeAgentManager, int, int) - Constructor for class etomica.models.co2.PNGCPM
PNGCPM.Component - Enum in etomica.models.co2
PNGCPM.GCPMAgent - Class in etomica.models.co2
PNGCPM.P3GCPMAxilrodTeller - Class in etomica.models.co2
PNGCPM.PNGCPMCached - Class in etomica.models.co2
PNGCPMCached() - Constructor for class etomica.models.co2.PNGCPM.PNGCPMCached
PNGCPMX - Class in etomica.models.co2: GCPM potential that allows combining parameters to be adjusted.
PNGCPMX(ISpace, AtomTypeAgentManager, int, double, double, double) - Constructor for class etomica.models.co2.PNGCPMX
PNGCPMX(ISpace, AtomTypeAgentManager, int, double, double, double, int) - Constructor for class etomica.models.co2.PNGCPMX
PNWaterGCPM - Class in etomica.models.water: GCPM Water potential class.
PNWaterGCPM(ISpace) - Constructor for class etomica.models.water.PNWaterGCPM
PNWaterGCPMThreeSite - Class in etomica.models.water: GCPM Water potential with three association site for Wertheim approach.
PNWaterGCPMThreeSite(ISpace, double, boolean, boolean) - Constructor for class etomica.models.water.PNWaterGCPMThreeSite
PNWaterGCPMThreeSite(ISpace, double, boolean) - Constructor for class etomica.models.water.PNWaterGCPMThreeSite
pochhammer(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Pochhammer's function.
Pochhammer(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Compute Pochhammer's symbol (this)_n.
Pochhammer(int) - Method in class etomica.veos.bigdecimal.Rational: Compute pochhammer's symbol (this)_n.
Point - Class in etomica.math.geometry: A zero-dimensional polytope, a mathematical point in space.
Point(ISpace) - Constructor for class etomica.math.geometry.Point
Point(ISpace, IVectorMutable) - Constructor for class etomica.math.geometry.Point
point - Static variable in class org.jmol.script.Token
Point3f - Class in org.jmol.util: A 3 element point that is represented by single precision floating point x,y,z coordinates.
Point3f() - Constructor for class org.jmol.util.Point3f
Point3fi - Class in org.jmol.util: the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points)
Point3fi() - Constructor for class org.jmol.util.Point3fi
Point3i - Class in org.jmol.util: A 3 element point that is represented by signed integer x,y,z coordinates.
Point3i() - Constructor for class org.jmol.util.Point3i
Point4f - Class in org.jmol.util: A 4 element point that is represented by single precision floating point x,y,z,w coordinates.
Point4f() - Constructor for class org.jmol.util.Point4f: Constructs and initializes a Point4f to (0,0,0,0).
pointCharges - Variable in class etomica.models.rowley.ConformationEthanol
pointCharges - Variable in class etomica.models.rowley.ConformationMethanol
pointCharges - Static variable in class etomica.models.rowley.DimerApproach
pointCharges - Variable in class etomica.models.rowley.SpeciesFactoryEthanol
pointCharges - Variable in class etomica.models.rowley.SpeciesFactoryMethanol
pointCharges - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
pointCount() - Method in class etomica.virial.cluster.ClusterDiagramTree
pointCount() - Method in interface etomica.virial.ClusterAbstract: Number of points in the cluster.
pointCount() - Method in class etomica.virial.ClusterBonds
pointCount() - Method in class etomica.virial.ClusterChainHS
pointCount() - Method in class etomica.virial.ClusterChainSoft
pointCount() - Method in class etomica.virial.ClusterCoupledFlipped
pointCount() - Method in class etomica.virial.ClusterCoupledFlippedPartial
pointCount() - Method in class etomica.virial.ClusterDifference
pointCount() - Method in class etomica.virial.ClusterExchange
pointCount() - Method in class etomica.virial.ClusterSinglyConnected
pointCount() - Method in class etomica.virial.ClusterSum
pointCount() - Method in class etomica.virial.ClusterSumHS
pointCount() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
pointCount() - Method in class etomica.virial.ClusterSumPolarizable
pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
pointCount() - Method in class etomica.virial.ClusterTree
pointCount() - Method in class etomica.virial.ClusterWeightAbs
pointCount() - Method in class etomica.virial.ClusterWeightSumWall
pointCount() - Method in class etomica.virial.ClusterWeightUmbrella
pointCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
pointCount() - Method in class etomica.virial.ClusterWheatleyHS
pointCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
pointCount() - Method in class etomica.virial.ClusterWheatleySoft
pointCount() - Method in class etomica.virial.ClusterWheatleySoftBD
pointgroupdistancetolerance - Static variable in class org.jmol.script.Token
pointgrouplineartolerance - Static variable in class org.jmol.script.Token
PointsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.PointsToggler
Poise - Class in etomica.units: The Poise unit of viscosity, equal to 1 gram/(cm-sec).
pol - Static variable in class etomica.models.water.P2WaterSzalewicz
polE1 - Variable in class etomica.models.water.P2WaterSzalewicz
polSite - Variable in class etomica.potential.P3Induction.MyAgent
Polygon - Class in etomica.math.geometry: Representation of a mathematical polygon, a 2-dimensional polytope.
Polygon(ISpace, int) - Constructor for class etomica.math.geometry.Polygon: Constructs a polygon with the given number of sides arranged in a closed loop.
Polygon(LineSegment[]) - Constructor for class etomica.math.geometry.Polygon: Constructs a polygon using the given edges for its sides.
polygonColixes - Variable in class org.jmol.util.MeshSurface
polygonCount - Variable in class org.jmol.util.MeshSurface
polygonCount0 - Variable in class org.jmol.util.MeshSurface
PolygonGeneral - Class in etomica.math.geometry: TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates
PolygonGeneral(ISpace, int) - Constructor for class etomica.math.geometry.PolygonGeneral
PolygonGeneral(LineSegment[]) - Constructor for class etomica.math.geometry.PolygonGeneral
polygonIndexes - Variable in class org.jmol.util.MeshSurface
polyhedra - Static variable in class org.jmol.script.Token
Polyhedron - Class in etomica.math.geometry: Representation of a mathematical polyhedron, a 3-dimensional polytope.
Polyhedron(Polygon[]) - Constructor for class etomica.math.geometry.Polyhedron: Constructs a polyhedron with the given faces for its sides.
PolyhedronGeneral - Class in etomica.math.geometry: Representation of a mathematical polyhedron, a 3-dimensional polytope.
PolyhedronGeneral(Polygon[]) - Constructor for class etomica.math.geometry.PolyhedronGeneral
polymer - Static variable in class org.jmol.script.Token
polymerlength - Static variable in class org.jmol.script.Token
polymerList - Variable in class etomica.modules.sam.CriterionTether3
polymerSpecies - Variable in class etomica.modules.sam.CriterionTether3
PolynomialFit - Class in etomica.util.numerical: Class that performs a polynomial fit to x,y data, optionally taking weights associated with each data point.
PolynomialFit() - Constructor for class etomica.util.numerical.PolynomialFit
polytope - Variable in class etomica.graphics.DisplayPolytope
Polytope - Class in etomica.math.geometry: Representation of a mathematical polytope, which is a finite region of space enclosed by a finite number of hyperplanes.
Polytope(Polytope[]) - Constructor for class etomica.math.geometry.Polytope: Constructs a polytope of dimension D from the D-1 finite "planes" that constitute it.
populate(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperBranched
populate(AtomArrayList, IAtom, IAtom, boolean) - Method in class etomica.association.AssociationHelperDouble
populate(MoleculeArrayList, IMolecule, boolean) - Method in class etomica.association.AssociationHelperMolecule
populateArrays(int, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
populateArrays(int, boolean) - Method in class etomica.overlap.DataOverlap
populateBonds(Graph, List<ClusterBonds>, List<Double>, boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
populateEFBonds(Graph, List<ClusterBonds>, List<Double>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
populateEFBonds(Graph, List<ClusterBonds>, List<Double>, int, int, boolean, boolean, int) - Method in class etomica.virial.cluster.VirialDiagramsMix2
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
populateEFdfdTBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
populateEFdfdTdf2dT2Bonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperBranched
populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperDouble
populateList(MoleculeArrayList, IMolecule, boolean) - Method in class etomica.association.AssociationHelperMolecule
populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperSingle
populateList(AtomArrayList, IAtom, boolean) - Method in interface etomica.association.IAssociationHelper: Populates smerList with all atoms in the smer that contains atom.
populateList(MoleculeArrayList, IMolecule, boolean) - Method in interface etomica.association.IAssociationHelperMolecule: Populates smerList with all molecules in the smer that contains molecule.
populateList(AtomArrayList) - Method in class etomica.association.MCMoveAtomMonomer
populateList(AtomArrayList) - Method in class etomica.association.MCMoveAtomSmer
populateList(AtomArrayList) - Method in class etomica.association.MCMoveBiasUB
populateList(AtomArrayList) - Method in class etomica.association.MCMoveRotateAssociated
populateList(AtomArrayList) - Method in class etomica.association.MCMoveSmer
populateList(AtomArrayList) - Method in class etomica.association.MCMoveSmerRotate
populateList(AtomArrayList, IAtom) - Method in class etomica.association.MCMoveVolumeAssociated
populateVDWDiameters(DiameterHashByElement) - Static method in class etomica.atom.DiameterHashByElement: Populates the given instance with diameters based on atomic radii (taken from various sources).
PopupListener(JPopupMenu) - Constructor for class etomica.graphics.DisplayPlot.PopupListener
popupMenu - Variable in class etomica.graphics.DisplayPlot.PopupListener
poreCenter - Variable in class etomica.modules.dcvgcmd.DCVGCMD
pos - Variable in class etomica.models.co2.P2CO2Hellmann
pos - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
pos - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
pos - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
pos - Variable in class etomica.normalmode.MeterPlaneSlip
pos - Variable in class etomica.potential.P2NitrogenHellmann
pos - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
pos - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
posA - Static variable in class etomica.models.co2.P2CO2Hellmann
posB - Static variable in class etomica.models.co2.P2CO2Hellmann
position - Variable in class etomica.atom.Atom
position(IMolecule) - Method in class etomica.atom.AtomPositionCOM
position(IMolecule) - Method in class etomica.atom.AtomPositionFirstAtom
position(IMolecule) - Method in class etomica.atom.AtomPositionGeometricCenter
position(IMolecule) - Method in class etomica.atom.AtomPositionGeometricCenterAlkaneEH
position(IMolecule) - Method in class etomica.atom.AtomPositionGeometricCenterPBC
position(IMolecule) - Method in interface etomica.atom.IAtomPositionDefinition: Returns the defined position for the given atom, which may be an atom group.
position - Variable in class etomica.atom.MoleculeOriented
position - Variable in class etomica.data.meter.MeterProfileByAtoms
position - Variable in class etomica.data.meter.MeterProfileByVolume
position - Variable in class etomica.math.geometry.Polytope
position - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
position - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
positionDefinition(IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
positionDefinition - Variable in class etomica.config.ConfigurationLattice
positionDefinition - Variable in class etomica.data.meter.MeterProfileByVolume
positionDefinition - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
positionDefinition - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
positionDefinition - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
positionDefinition - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
positionDefinition - Variable in class etomica.models.water.P2Water4P
positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
positionDefinition - Variable in class etomica.modules.rosmosis.MeterFlux
positionDefinition - Variable in class etomica.modules.sam.Sam
positionDefinition - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
positionDefinition - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
positionDefinition - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
positionDefinition - Variable in class etomica.nbr.cell.NeighborCellManager
positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
positionDefinition - Variable in class etomica.potential.P2MoleculeTruncated
positionDefinition - Variable in class etomica.potential.P2ReactionFieldDipole
positionDefinition - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
positionDefinition - Variable in class etomica.potential.PotentialGroupSoft
positionDefinition - Variable in class etomica.virial.ClusterCoupledFlipped
positionDefinition - Variable in class etomica.virial.ClusterCoupledFlippedPartial
positionDefinition - Variable in class etomica.virial.CoordinatePairMoleculeSet
positionDefinition - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
positionDefinition - Variable in class etomica.virial.MCMoveClusterTorsionMulti
positionOld - Variable in class etomica.models.hexane.MCMoveCBMC
positions - Variable in class etomica.dimer.SimDimerLJadatom
positions - Variable in class etomica.dimer.SimDimerMEAMadatom
positions - Variable in class etomica.dimer.SimDimerMEAMGB
positions - Variable in class etomica.kmc.SimKMCMEAMadatom
positions - Variable in class etomica.virial.CoordinatePairLeafSet
positionSelectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
positionSource - Variable in class etomica.data.meter.MeterProfile
positionSource - Variable in class etomica.data.meter.MeterWidomInsertion
positionSource - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
positionSource - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
positionSource - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
positionSource - Variable in class etomica.liquidLJ.MeterWidomInsertionP
positionSource - Variable in class etomica.models.hexane.CBMCGrowStraightAlkane
positionVector - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
positionVector - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
posVec - Static variable in class etomica.potential.P2WaterPotentialsJankowski
posVecToAtoms(IVectorMutable[], IVectorMutable[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
pot - Variable in class etomica.virial.PotentialCommonAtomic
poten() - Static method in class etomica.potential.P2WaterPotentialsJankowski
potential - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
potential - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
potential - Variable in class etomica.association.TestLJAssociationMC3D_NPT
potential - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
potential - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
potential - Variable in class etomica.data.meter.MeterEnergy
potential - Variable in class etomica.data.meter.MeterPotentialEnergy
potential - Variable in class etomica.densityofstate.DensityOfState
potential - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
potential - Variable in class etomica.dimer.EnergyMap
potential - Variable in class etomica.dimer.SimDimerLJgb
potential - Variable in class etomica.dimer.SimDimerMEAMadatom
potential - Variable in class etomica.dimer.SimDimerMEAMGB
potential - Variable in class etomica.freeenergy.npath.SimIdealGas
potential - Variable in class etomica.freeenergy.npath.SimLJ
potential - Variable in class etomica.integrator.mcmove.MCMove
potential - Variable in class etomica.kmc.SimKMCMEAMadatom
potential - Variable in class etomica.liquidLJ.LjMC3D
potential - Variable in class etomica.liquidLJ.LjMd3D
potential - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
potential - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
potential - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
potential - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
potential - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potential - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
potential - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
potential - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
potential - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
potential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
potential - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
potential - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
potential - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
potential - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
potential - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
potential - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
potential - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
potential - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
potential - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
potential - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
potential - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
potential - Variable in class etomica.normalmode.LJVacancyMin
potential - Variable in class etomica.normalmode.MCMoveAtomSuperBox
potential - Variable in class etomica.normalmode.MeterAPIPotentialEnergy
potential - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
potential - Variable in class etomica.normalmode.SimHSMDVacancy
potential - Variable in class etomica.normalmode.SimLJHTTISuper
potential - Variable in class etomica.normalmode.SimLJHTTISuperHCP
potential - Variable in class etomica.normalmode.SimLJVacancy
potential - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
potential - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
potential - Variable in class etomica.potential.P2MoleculeTruncated
potential - Variable in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
potential - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
potential - Variable in class etomica.potential.P2SoftSphericalTruncated
potential - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
Potential - Class in etomica.potential: Superclass for all Potential classes, which define how the atoms in the system interact with each other.
Potential(int, ISpace) - Constructor for class etomica.potential.Potential: General constructor for a potential instance
potential - Variable in class etomica.potential.PotentialGroup.PotentialLinker
potential - Variable in class etomica.potential.PotentialMaster.PotentialLinker
potential - Variable in class etomica.simulation.prototypes.ChainHSMD3D
potential - Variable in class etomica.simulation.prototypes.GEMCWithRotation
potential - Variable in class etomica.simulation.prototypes.HsMc2d
potential - Variable in class etomica.simulation.prototypes.HSMD3D: The hard-sphere potential governing the interactions.
potential - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
potential - Variable in class etomica.simulation.prototypes.LjMd2D
potential - Variable in class etomica.simulation.prototypes.LjMd3D
potential - Variable in class etomica.simulation.prototypes.SoftSphere3d
potential - Variable in class etomica.simulation.prototypes.SwMd2D
potential - Variable in class etomica.simulation.prototypes.SWMD3D
potential - Variable in class etomica.spin.Heisenberg
potential - Variable in class etomica.tests.TestLJMC3D
potential - Variable in class etomica.thermointegration.LjMc3D
potential - Variable in class etomica.threaded.atom.LJMD3DThreaded
potential - Variable in class etomica.threaded.domain.LJMD3DThreaded
potential - Variable in class etomica.threaded.PotentialThreaded
potential - Variable in class etomica.virial.MayerGeneralAtomic
potential - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
potential - Variable in class etomica.yukawa.TestHC2YukawaMC3D
potential - Variable in class etomica.yukawa.TestYukawaMC3D
potential - Variable in class etomica.yukawa.TestYukawaMD3D
Potential0 - Class in etomica.potential: Potential that does not depend on any atom positions.
Potential0(ISpace) - Constructor for class etomica.potential.Potential0
Potential0Lrc - Class in etomica.potential: Zero-body potential implementing the long-range correction that compensates for truncation of the potential.
Potential0Lrc(ISpace, IAtomType[], IPotentialAtomic) - Constructor for class etomica.potential.Potential0Lrc
potential1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
Potential1 - Class in etomica.potential: Potential acting on a single atom or atom group.
Potential1(ISpace) - Constructor for class etomica.potential.Potential1
Potential1.Intramolecular - Interface in etomica.potential: Marker interface indicating that a one-body potential is an intramolecular potential, and not, e.g., a potential of interaction with an external field.
potential11 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potential11 - Variable in class etomica.simulation.prototypes.HSMD2D
potential12 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potential12 - Variable in class etomica.simulation.prototypes.HSMD2D
Potential2 - Class in etomica.potential: Potential acting on 2 atoms or molecules.
Potential2(ISpace) - Constructor for class etomica.potential.Potential2: Constructs potential with given space.
potential22 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potential22 - Variable in class etomica.simulation.prototypes.HSMD2D
Potential2HardSpherical - Class in etomica.potential: Methods for a hard (impulsive), spherically-symmetric pair potential.
Potential2HardSpherical(ISpace) - Constructor for class etomica.potential.Potential2HardSpherical
Potential2Soft - Interface in etomica.potential: Methods for properties obtained for a soft, differentiable pair potential.
Potential2SoftSpherical - Class in etomica.potential: Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSpherical(ISpace) - Constructor for class etomica.potential.Potential2SoftSpherical
Potential2SoftSphericalLS - Class in etomica.potential: Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLS(ISpace, double, double[], Potential2Soft) - Constructor for class etomica.potential.Potential2SoftSphericalLS
Potential2SoftSphericalLSMulti - Class in etomica.liquidLJ: Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLSMulti(ISpace, double[], Potential2Soft) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMulti
Potential2SoftSphericalLSMultiLat - Class in etomica.liquidLJ: Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLSMultiLat(ISpace, double[], Potential2Soft, CoordinateDefinition) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
Potential2SoftSphericalLSMultiLat.ReturnValue - Class in etomica.liquidLJ
Potential2SoftSphericalLSMultiLatSlanty - Class in etomica.liquidLJ: Methods for a soft (non-impulsive), spherically-symmetric pair potential.
Potential2SoftSphericalLSMultiLatSlanty(ISpace, double[], Potential2Soft, CoordinateDefinition, int[]) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
Potential2Spherical - Interface in etomica.potential: interface for spherical 2-body potentials
potentialA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
potentialA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
potentialA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
potentialA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
potentialA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
potentialAA - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
potentialAA - Variable in class etomica.modules.mu.Mu
potentialAA - Variable in class etomica.modules.osmosis.OsmosisSim
potentialAB - Variable in class etomica.modules.mu.Mu
potentialAB - Variable in class etomica.modules.osmosis.OsmosisSim
potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in interface etomica.api.IPotentialMaster: Notifies the PotentialMaster that the sub-potential has been added to the given PotentialGroup, which is associated (but not necessarily held by) this PotentialMaster.
potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.nbr.PotentialMasterHybrid
potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.nbr.PotentialMasterNbr
potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.potential.PotentialMaster
potentialAgentManager - Variable in class etomica.potential.PotentialMasterMonatomic
PotentialAndIterator(IPotentialAtomic, AtomsetIteratorBasisDependent) - Constructor for class etomica.chem.models.Model.PotentialAndIterator
PotentialArray - Class in etomica.potential: Instances of this class are created by AtomType classes to store the list of potentials and criteria that apply to the atoms of that type.
PotentialArray() - Constructor for class etomica.potential.PotentialArray
PotentialArrayByType - Class in etomica.potential: This class stores an array of Potentials and remembers the "other" IAtomType that the IPotential applies to.
PotentialArrayByType() - Constructor for class etomica.potential.PotentialArrayByType
PotentialArrayMolecular - Class in etomica.potential: Instances of this class are created by MoleculeType classes to store the list of potentials and criteria that apply to the molecules of that type.
PotentialArrayMolecular() - Constructor for class etomica.potential.PotentialArrayMolecular
potentialAtomic - Variable in class etomica.potential.PotentialMolecularMonatomic
PotentialAtomicSum - Class in etomica.potential: Atomic potential class that simply sums up contributions from multiple (atomic) potentials.
PotentialAtomicSum(IPotentialAtomic[]) - Constructor for class etomica.potential.PotentialAtomicSum
potentialAtt - Variable in class etomica.virial.MayerPTAtt
potentialAtt - Variable in class etomica.virial.MayerSphericalPTAtt
potentialB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
potentialB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
potentialB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
potentialB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
potentialB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
potentialBB - Variable in class etomica.modules.mu.Mu
potentialBB - Variable in class etomica.modules.osmosis.OsmosisSim
potentialBonded - Variable in class etomica.modules.render.RenderMD
PotentialCalculation - Interface in etomica.potential: Class defining a particular action to be performed on a set of atoms using an arbitrary potential.
PotentialCalculationEFSSP - Class in etomica.normalmode
PotentialCalculationEFSSP(ISpace, IBox, CoordinateDefinition, double, double, boolean) - Constructor for class etomica.normalmode.PotentialCalculationEFSSP
PotentialCalculationEnergies() - Constructor for class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
PotentialCalculationEnergySum - Class in etomica.potential: Evaluates the energy summed over all iterated atoms.
PotentialCalculationEnergySum() - Constructor for class etomica.potential.PotentialCalculationEnergySum
PotentialCalculationEnergySumBigDecimal - Class in etomica.potential: Mimics original PotentialEnergySum calculation, but uses a BigDecimal representation for the sum.
PotentialCalculationEnergySumBigDecimal(int) - Constructor for class etomica.potential.PotentialCalculationEnergySumBigDecimal
PotentialCalculationEnergySumCutoff - Class in etomica.liquidLJ: Evaluates the energy summed over all iterated atoms.
PotentialCalculationEnergySumCutoff(ISpace, double[]) - Constructor for class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
PotentialCalculationForcePressureSum - Class in etomica.potential: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
PotentialCalculationForcePressureSum(ISpace) - Constructor for class etomica.potential.PotentialCalculationForcePressureSum
PotentialCalculationForcePressureSumGB - Class in etomica.dimer: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
PotentialCalculationForcePressureSumGB(ISpace, IBox) - Constructor for class etomica.dimer.PotentialCalculationForcePressureSumGB
PotentialCalculationForceStress - Class in etomica.modules.materialfracture
PotentialCalculationForceStress(ISpace) - Constructor for class etomica.modules.materialfracture.PotentialCalculationForceStress
PotentialCalculationForceSum - Class in etomica.potential: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
PotentialCalculationForceSum() - Constructor for class etomica.potential.PotentialCalculationForceSum
PotentialCalculationForceSumThreaded - Class in etomica.threaded
PotentialCalculationForceSumThreaded(PotentialCalculationForceSum[], ISpace) - Constructor for class etomica.threaded.PotentialCalculationForceSumThreaded
PotentialCalculationForceSumWall - Class in etomica.modules.sam
PotentialCalculationForceSumWall(P1WCAWall) - Constructor for class etomica.modules.sam.PotentialCalculationForceSumWall
PotentialCalculationForceSumWallForce - Class in etomica.modules.rosmosis: Sums the force and torque on each iterated atom or molecule and adds it to the agent associated with the atom.
PotentialCalculationForceSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
PotentialCalculationHyperVirialSum - Class in etomica.potential: Evaluates the hypervirial summed over all iterated atoms.
PotentialCalculationHyperVirialSum() - Constructor for class etomica.potential.PotentialCalculationHyperVirialSum
PotentialCalculationLJSP - Class in etomica.normalmode
PotentialCalculationLJSP(ISpace, IBox, CoordinateDefinition, double, double, double, double, double) - Constructor for class etomica.normalmode.PotentialCalculationLJSP
PotentialCalculationMappedVirial - Class in etomica.mappedvirial: PotentialCalculation that implements mapped-averaged virial (to get the pressure).
PotentialCalculationMappedVirial(ISpace, IBox, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirial
PotentialCalculationMappedVirialV - Class in etomica.mappedvirial: PotentialCalculation that implements mapped-averaged virial (to get the pressure).
PotentialCalculationMappedVirialV(ISpace, IBox, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV
PotentialCalculationMappedVirialV.UShift - Class in etomica.mappedvirial
PotentialCalculationMappedVirialV.USine - Class in etomica.mappedvirial
PotentialCalculationMappedVirialV.VFunc - Interface in etomica.mappedvirial
PotentialCalculationMolecular - Interface in etomica.potential: Class defining a particular action to be performed on a set of atoms using an arbitrary potential.
PotentialCalculationMolecularVirialSum - Class in etomica.potential: Evaluates the virial summed over all iterated molecules.
PotentialCalculationMolecularVirialSum() - Constructor for class etomica.potential.PotentialCalculationMolecularVirialSum
PotentialCalculationPhiSum - Class in etomica.potential
PotentialCalculationPhiSum(ISpace) - Constructor for class etomica.potential.PotentialCalculationPhiSum
PotentialCalculationPressureTensor - Class in etomica.potential: Calculates the pressure tensor by calculating the force on each atom, along with including the kinetic portion (from the velocities or an Integrator).
PotentialCalculationPressureTensor(ISpace) - Constructor for class etomica.potential.PotentialCalculationPressureTensor
PotentialCalculationRDF - Class in etomica.data.meter: PotentialCalculation that simply does the work of collecting an RDF.
PotentialCalculationRDF(ISpace, IBox) - Constructor for class etomica.data.meter.PotentialCalculationRDF
PotentialCalculationSolidSuper - Class in etomica.normalmode: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
PotentialCalculationSolidSuper(ISpace, CoordinateDefinition) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuper
PotentialCalculationSolidSuperCut - Class in etomica.normalmode: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
PotentialCalculationSolidSuperCut(ISpace, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuperCut
PotentialCalculationSolidSuperCutLS - Class in etomica.normalmode: Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
PotentialCalculationSolidSuperCutLS(ISpace, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuperCutLS
PotentialCalculationSumCutoff - Class in etomica.liquidLJ: Evaluates the energy summed over all iterated atoms.
PotentialCalculationSumCutoff(ISpace, double[]) - Constructor for class etomica.liquidLJ.PotentialCalculationSumCutoff
PotentialCalculationSumCutoffLS - Class in etomica.liquidLJ: Evaluates the energy summed over all iterated atoms.
PotentialCalculationSumCutoffLS() - Constructor for class etomica.liquidLJ.PotentialCalculationSumCutoffLS
PotentialCalculationTorqueSum - Class in etomica.potential: Sums the force and torque on each iterated atom or molecule and adds it to the agent associated with the atom.
PotentialCalculationTorqueSum() - Constructor for class etomica.potential.PotentialCalculationTorqueSum
PotentialCalculationTorqueSumWallForce - Class in etomica.modules.rosmosis: Sums the force and torque on each iterated atom or molecule and adds it to the agent associated with the atom.
PotentialCalculationTorqueSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
PotentialCalculationVirialSum - Class in etomica.potential: Evaluates the virial summed over all iterated atoms.
PotentialCalculationVirialSum() - Constructor for class etomica.potential.PotentialCalculationVirialSum
PotentialCalculationWallForce() - Constructor for class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
potentialCC - Variable in class etomica.modules.catalysis.Catalysis
potentialCC - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialCC - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialChoice - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
potentialChooser - Variable in class etomica.modules.insertion.InsertionGraphic
potentialChooser - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
potentialChooser - Variable in class etomica.modules.swmd.SwmdGraphic
potentialChooserListener - Variable in class etomica.modules.insertion.InsertionGraphic
potentialChooserListener - Variable in class etomica.modules.mu.MuGraphic
potentialChooserListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
potentialChooserListener - Variable in class etomica.modules.swmd.SwmdGraphic
potentialCHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialCHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialCHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialCHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialCN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialCN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialCO - Variable in class etomica.modules.catalysis.Catalysis
potentialCO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialCO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
PotentialCommonAtomic - Class in etomica.virial
PotentialCommonAtomic(IPotentialAtomic) - Constructor for class etomica.virial.PotentialCommonAtomic
PotentialCriterion() - Constructor for class etomica.atom.iterator.IteratorDirective.PotentialCriterion
potentialCS - Variable in class etomica.modules.catalysis.Catalysis
potentialCS - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
PotentialCuLREP - Class in etomica.meam
PotentialCuLREP(ISpace) - Constructor for class etomica.meam.PotentialCuLREP
PotentialDLPOLY - Class in etomica.potential
PotentialDLPOLY(ISpace) - Constructor for class etomica.potential.PotentialDLPOLY
PotentialEFS - Class in etomica.meam: EFS (Extended Finnis-Sinclair) potential
PotentialEFS(ISpace, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.meam.PotentialEFS
PotentialEmul - Class in etomica.potential: PotentialEmul class invokes the emul external program to compute energies between molecules.
PotentialEmul(ISpace, String) - Constructor for class etomica.potential.PotentialEmul
PotentialEmul(ISpace, String, double) - Constructor for class etomica.potential.PotentialEmul
PotentialEmul(ISpace, String, int, double) - Constructor for class etomica.potential.PotentialEmul
PotentialEmulCached - Class in etomica.virial: Potential class whose sole purpose is to remember previously calculated energies and return them if no change has been made to the configuration.
PotentialEmulCached(ISpace, String, int) - Constructor for class etomica.virial.PotentialEmulCached
PotentialEmulCached(ISpace, String, double, int) - Constructor for class etomica.virial.PotentialEmulCached
PotentialEmulCached(ISpace, String, int, double, int) - Constructor for class etomica.virial.PotentialEmulCached
potentialES - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
potentialES - Variable in class etomica.models.clathrates.MinimizationTIP4P
PotentialFeEAM - Class in etomica.meam: EFS (Extended Finnis-Sinclair) potential
PotentialFeEAM(ISpace, double, double, double, double, double, double) - Constructor for class etomica.meam.PotentialFeEAM
PotentialFeEAM_LS - Class in etomica.meam: EFS (Extended Finnis-Sinclair) potential
PotentialFeEAM_LS(CoordinateDefinition, ISpace, double, double, double, double, double, double, IVector[]) - Constructor for class etomica.meam.PotentialFeEAM_LS
potentialGhost - Variable in class etomica.modules.insertion.Insertion
PotentialGroup - Class in etomica.potential: Collection of potentials that act between the atoms contained in one or more groups of atoms.
PotentialGroup(int) - Constructor for class etomica.potential.PotentialGroup: Makes a potential group defined on the position of nBody atom or atom groups.
PotentialGroup(int, ISpace) - Constructor for class etomica.potential.PotentialGroup
PotentialGroup.PotentialLinker - Class in etomica.potential
PotentialGroup3PI - Class in etomica.virial: PotentialGroup that calculates the energy between PI molecules triplets.
PotentialGroup3PI(int) - Constructor for class etomica.virial.PotentialGroup3PI
PotentialGroup3PI.PotentialGroup3PISkip - Class in etomica.virial
PotentialGroup3PISkip(int) - Constructor for class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
PotentialGroupHybrid - Class in etomica.nbr: A PotentialGroup class to work with PotentialMasterHybrid.
PotentialGroupHybrid(int) - Constructor for class etomica.nbr.PotentialGroupHybrid
PotentialGroupNbr - Class in etomica.nbr
PotentialGroupNbr(int) - Constructor for class etomica.nbr.PotentialGroupNbr
PotentialGroupPI - Class in etomica.virial: PotentialGroup that calculates the energy between PI molecule pairs.
PotentialGroupPI(int) - Constructor for class etomica.virial.PotentialGroupPI
PotentialGroupPI.PotentialGroupPISkip - Class in etomica.virial
PotentialGroupPISkip(int) - Constructor for class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
PotentialGroupSoft - Class in etomica.potential: include virial and gradient for a molecular potential
PotentialGroupSoft(int, ISpace, double) - Constructor for class etomica.potential.PotentialGroupSoft
PotentialHard - Interface in etomica.potential: Interface for hard potentials, having impulsive forces.
potentialHpHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialHpHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialHpN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialHpN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialHS - Variable in class etomica.modules.insertion.InsertionGraphic
potentialHS - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
potentialHS - Variable in class etomica.modules.swmd.SwmdGraphic
potentialHyHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialHyHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialHyHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialHyHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialHyN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialHyN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialHyO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialHyO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialIdeal - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
potentialIdeal - Variable in class etomica.modules.swmd.SwmdGraphic
potentialIterator - Variable in class etomica.potential.PotentialMasterMonatomic
potentialLevel - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
potentialLevel - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
potentialLevel - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
potentialLevel - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
PotentialLinker(IPotentialAtomic, AtomsetIteratorBasisDependent, IAtomType[], PotentialGroup.PotentialLinker) - Constructor for class etomica.potential.PotentialGroup.PotentialLinker
PotentialLinker(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) - Constructor for class etomica.potential.PotentialMaster.PotentialLinker
potentialList - Variable in class etomica.potential.PotentialMaster
potentialLJ - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
potentialLJClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialLJLS - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
potentialLJLS - Variable in class etomica.models.clathrates.MinimizationTIP4P
potentialLJNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialLJNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialLJOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialLJONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialM1 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potentialM2 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potentialMaster - Variable in class etomica.AlkaneEH.CH4NVT
potentialMaster - Variable in class etomica.AlkaneEH.DHS_NVT
potentialMaster - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
potentialMaster - Variable in class etomica.association.MCMoveDimer
potentialMaster - Variable in class etomica.association.MCMoveDimerRotate
potentialMaster - Variable in class etomica.association.MCMoveSmer
potentialMaster - Variable in class etomica.association.MCMoveSmerRotate
potentialMaster - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
potentialMaster - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
potentialMaster - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
potentialMaster - Variable in class etomica.data.meter.MeterHyperVirial
potentialMaster - Variable in class etomica.data.meter.MeterPressure
potentialMaster - Variable in class etomica.data.meter.MeterPressureTensor
potentialMaster - Variable in class etomica.data.meter.MeterRDFPC
potentialMaster - Variable in class etomica.densityofstate.DensityOfState
potentialMaster - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
potentialMaster - Variable in class etomica.dielectric.DHS_NVT
potentialMaster - Variable in class etomica.dielectric.DLJ_NVT_1site
potentialMaster - Variable in class etomica.dielectric.TIP4P_NVT
potentialMaster - Variable in class etomica.dimer.EnergyMap
potentialMaster - Variable in class etomica.dimer.SimDimerLJadatom
potentialMaster - Variable in class etomica.dimer.SimDimerLJgb
potentialMaster - Variable in class etomica.dimer.SimDimerMEAMadatom
potentialMaster - Variable in class etomica.dimer.SimDimerMEAMGB
potentialMaster - Variable in class etomica.freeenergy.npath.DataSourceEnergies
potentialMaster - Variable in class etomica.integrator.IntegratorBox
potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveDimer
potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
potentialMaster - Variable in class etomica.interfacial.LJMD
potentialMaster - Variable in class etomica.interfacial.MeterWallForce
potentialMaster - Variable in class etomica.kmc.SimKMCLJadatom
potentialMaster - Variable in class etomica.liquidLJ.MeterPU
potentialMaster - Variable in class etomica.liquidLJ.MeterPUCut
potentialMaster - Variable in class etomica.liquidLJ.MeterPUCutLS
potentialMaster - Variable in class etomica.mappedvirial.MeterMappedU
potentialMaster - Variable in class etomica.mappedvirial.MeterMappedVirial
potentialMaster - Variable in class etomica.mappedvirial.MeterMappedVirialV
potentialMaster - Variable in class etomica.mappedvirial.MeterMeanForce
potentialMaster - Variable in class etomica.meam.EFSTungsten
potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithGB
potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
potentialMaster - Variable in class etomica.meam.MEAM_MC
potentialMaster - Variable in class etomica.meam.MEAMMd3D
potentialMaster - Variable in class etomica.metastable.LJmuVT
potentialMaster - Variable in class etomica.metastable.LJNPT
potentialMaster - Variable in class etomica.metastable.LJNVT
potentialMaster - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
potentialMaster - Variable in class etomica.models.clathrates.MinimizationTIP4P
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
potentialMaster - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
potentialMaster - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
potentialMaster - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
potentialMaster - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
potentialMaster - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
potentialMaster - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
potentialMaster - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
potentialMaster - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
potentialMaster - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
potentialMaster - Variable in class etomica.models.rowley.DimerApproach
potentialMaster - Variable in class etomica.models.water.TestEwaldTIP4PWater
potentialMaster - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
potentialMaster - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
potentialMaster - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
potentialMaster - Variable in class etomica.modules.colloid.ColloidSim
potentialMaster - Variable in class etomica.modules.droplet.DropletAtomic
potentialMaster - Variable in class etomica.modules.mu.P1MagicWall
potentialMaster - Variable in class etomica.modules.render.RenderMD
potentialMaster - Variable in class etomica.modules.sam.ConfigurationSAM
potentialMaster - Variable in class etomica.modules.sam.Sam
potentialMaster - Variable in class etomica.modules.vle.MeterPressure2
potentialMaster - Variable in class etomica.nbr.list.BoxAgentSourceCellManagerList
potentialMaster - Variable in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
potentialMaster - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
potentialMaster - Variable in class etomica.nbr.list.NeighborCellManagerList
potentialMaster - Variable in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
potentialMaster - Variable in class etomica.nbr.list.NeighborListManager
potentialMaster - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
potentialMaster - Variable in class etomica.normalmode.HessianDB
potentialMaster - Variable in class etomica.normalmode.HSDimerNPT
potentialMaster - Variable in class etomica.normalmode.HSNPT
potentialMaster - Variable in class etomica.normalmode.HTTPSoftSphereSim
potentialMaster - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
potentialMaster - Variable in class etomica.normalmode.LJVacancyMin
potentialMaster - Variable in class etomica.normalmode.MeterBoltzmannHTTP
potentialMaster - Variable in class etomica.normalmode.MeterDADB
potentialMaster - Variable in class etomica.normalmode.MeterDDP
potentialMaster - Variable in class etomica.normalmode.MeterDP
potentialMaster - Variable in class etomica.normalmode.MeterSolidDA
potentialMaster - Variable in class etomica.normalmode.MeterSolidDACut
potentialMaster - Variable in class etomica.normalmode.MeterSolidProps
potentialMaster - Variable in class etomica.normalmode.MeterSolidPropsLJ
potentialMaster - Variable in class etomica.normalmode.MeterTargetTP
potentialMaster - Variable in class etomica.normalmode.MinimizeHCP
potentialMaster - Variable in class etomica.normalmode.NormalModesMolecular
potentialMaster - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
potentialMaster - Variable in class etomica.normalmode.SimCalcSLJ
potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
potentialMaster - Variable in class etomica.normalmode.SimEinStep1
potentialMaster - Variable in class etomica.normalmode.SimEinStep1HCP
potentialMaster - Variable in class etomica.normalmode.SimEinStep2
potentialMaster - Variable in class etomica.normalmode.SimEinStep2HCP
potentialMaster - Variable in class etomica.normalmode.SimFluidSoftSphere
potentialMaster - Variable in class etomica.normalmode.SimLJHTTISuper
potentialMaster - Variable in class etomica.normalmode.SimLJHTTISuperHCP
potentialMaster - Variable in class etomica.normalmode.SimLJVacancy
potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
potentialMaster - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
potentialMaster - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialMaster - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
potentialMaster - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
potentialMaster - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
potentialMaster - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
potentialMaster - Variable in class etomica.potential.P2SquareWellRobust
potentialMaster - Variable in class etomica.potential.PotentialGroup
PotentialMaster - Class in etomica.potential: Manager of all potentials in simulation.
PotentialMaster() - Constructor for class etomica.potential.PotentialMaster
PotentialMaster(IteratorFactory) - Constructor for class etomica.potential.PotentialMaster
potentialMaster - Variable in class etomica.simulation.prototypes.HSMD3D
potentialMaster - Variable in class etomica.simulation.prototypes.SoftSphere3d
potentialMaster - Variable in class etomica.spin.Heisenberg
potentialMaster - Variable in class etomica.surfacetension.LJMC
potentialMaster - Variable in class etomica.surfacetension.SurfaceTensionMapped
potentialMaster - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
potentialMaster - Variable in class etomica.util.numerical.CalcGradientDifferentiable
PotentialMaster.AtomIterator0 - Class in etomica.potential
PotentialMaster.MoleculeIterator0 - Class in etomica.potential
PotentialMaster.PotentialLinker - Class in etomica.potential
potentialMasterA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
potentialMasterA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
potentialMasterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
potentialMasterB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
potentialMasterB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
potentialMasterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
potentialMasterCell - Variable in class etomica.freeenergy.npath.SimIdealGas
potentialMasterCell - Variable in class etomica.freeenergy.npath.SimLJ
potentialMasterCell - Variable in class etomica.interfacial.LJMC
potentialMasterCell - Variable in class etomica.liquidLJ.LjMC3D
PotentialMasterCell - Class in etomica.nbr.cell: A PotentialMaster for use with a Simulation where cell-listing of atoms and their neighbors is appropriate.
PotentialMasterCell(ISimulation, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell: Creates PotentialMasterCell with default (1.0) range.
PotentialMasterCell(ISimulation, double, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell: Constructs with null AtomPositionDefinition, which indicates the position definition given with each atom's AtomType should be used.
PotentialMasterCell(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
PotentialMasterCell(ISimulation, double, BoxAgentSourceCellManager, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
PotentialMasterCell(ISimulation, double, BoxAgentSourceCellManager, BoxAgentManager<NeighborCellManager>, ISpace) - Constructor for class etomica.nbr.cell.PotentialMasterCell
potentialMasterCell - Variable in class etomica.nbr.PotentialGroupHybrid
potentialMasterD - Variable in class etomica.dimer.SimDimerMEAMadatom
potentialMasterD - Variable in class etomica.dimer.SimDimerMEAMGB
potentialMasterD - Variable in class etomica.kmc.SimKMCMEAMadatom
potentialMasterDADv2 - Variable in class etomica.liquidLJ.MeterPUCut
potentialMasterDADv2 - Variable in class etomica.liquidLJ.MeterPUCutLS
potentialMasterDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep1
potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep1HCP
potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep2
potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep2HCP
potentialMasterHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
potentialMasterHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
PotentialMasterHybrid - Class in etomica.nbr: PotentialMaster that uses both neighbor-cell iteration and cell-list iteration.
PotentialMasterHybrid(ISimulation, double, ISpace) - Constructor for class etomica.nbr.PotentialMasterHybrid: Invokes superclass constructor, specifying IteratorFactoryCell for generating molecule iterators.
PotentialMasterHybrid(ISimulation, IAtomPositionDefinition, double, ISpace) - Constructor for class etomica.nbr.PotentialMasterHybrid: Constructs class using given position definition for all atom cell assignments.
potentialMasterList - Variable in class etomica.liquidLJ.LjMd3D
PotentialMasterList - Class in etomica.nbr.list: PotentialMaster used to implement neighbor listing.
PotentialMasterList(ISimulation, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList: Default constructor uses range of 1.0.
PotentialMasterList(ISimulation, double, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList: Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
PotentialMasterList(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList: Constructs class using given position definition for all atom cell assignments.
PotentialMasterList(ISimulation, double, BoxAgentSourceCellManagerList, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
PotentialMasterList(ISimulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<? extends BoxCellManager>, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
PotentialMasterList(ISimulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<? extends BoxCellManager>, PotentialMasterList.NeighborListAgentSource, ISpace) - Constructor for class etomica.nbr.list.PotentialMasterList
potentialMasterList - Variable in class etomica.nbr.PotentialGroupHybrid
potentialMasterList - Variable in class etomica.normalmode.SimHSMDVacancy
PotentialMasterList.NeighborListAgentSource - Class in etomica.nbr.list
PotentialMasterListDimer - Class in etomica.dimer
PotentialMasterListDimer(ISimulation, ISpace) - Constructor for class etomica.dimer.PotentialMasterListDimer
PotentialMasterListMolecular - Class in etomica.nbr.list.molecule: PotentialMaster used to implement neighbor listing.
PotentialMasterListMolecular(ISimulation, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular: Default constructor uses range of 1.0.
PotentialMasterListMolecular(ISimulation, double, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular: Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
PotentialMasterListMolecular(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular: Constructs class using given position definition for all atom cell assignments.
PotentialMasterListMolecular(ISimulation, double, BoxAgentSourceCellManagerListMolecular, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
PotentialMasterListMolecular(ISimulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
PotentialMasterListMolecular(ISimulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, PotentialMasterListMolecular.NeighborListAgentSourceMolecular, ISpace) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
PotentialMasterListMolecular.NeighborListAgentSourceMolecular - Class in etomica.nbr.list.molecule
PotentialMasterListThreaded - Class in etomica.threaded.atom
PotentialMasterListThreaded(ISimulation, ISpace) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, ISpace, double) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, ISpace, double, IAtomPositionDefinition) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, ISpace, double, BoxAgentSourceCellManagerList) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, ISpace, double, BoxAgentSourceCellManagerList, BoxAgentManager) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
PotentialMasterListThreaded - Class in etomica.threaded.domain
PotentialMasterListThreaded(ISimulation, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, double, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, double, IAtomPositionDefinition, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, double, BoxAgentSourceCellManagerList, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
PotentialMasterListThreaded(ISimulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<NeighborCellManager>, ISpace) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
PotentialMasterListThreaded.NeighborListAgentSourceThreaded - Class in etomica.threaded.domain
PotentialMasterListWorker - Class in etomica.threaded.atom
PotentialMasterListWorker(int, AtomTypeAgentManager, PotentialMasterListThreaded) - Constructor for class etomica.threaded.atom.PotentialMasterListWorker
PotentialMasterListWorker - Class in etomica.threaded.domain
PotentialMasterListWorker(int, AtomTypeAgentManager, PotentialMasterListThreaded) - Constructor for class etomica.threaded.domain.PotentialMasterListWorker
potentialMasterLong - Variable in class etomica.liquidLJ.LjMd3D
potentialMasterLongCut - Variable in class etomica.liquidLJ.LjMd3D
PotentialMasterLrc - Class in etomica.potential: Collects potentials used for long-range correction.
PotentialMasterLrc() - Constructor for class etomica.potential.PotentialMasterLrc
potentialMasterMonatomic - Variable in class etomica.normalmode.SimBennet
potentialMasterMonatomic - Variable in class etomica.normalmode.SimHarmonicUmbrella
potentialMasterMonatomic - Variable in class etomica.normalmode.SimTargetUmbrella
potentialMasterMonatomic - Variable in class etomica.normalmode.SimUmbrella
PotentialMasterMonatomic - Class in etomica.potential: PotentialMaster suitable for monatomic molecules without using neighbor lists and avoids PotentialMaster's performance problems.
PotentialMasterMonatomic(ISimulation) - Constructor for class etomica.potential.PotentialMasterMonatomic
PotentialMasterNbr - Class in etomica.nbr
PotentialMasterNbr(ISimulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>) - Constructor for class etomica.nbr.PotentialMasterNbr
PotentialMasterNbrMolecular - Class in etomica.nbr.molecule
PotentialMasterNbrMolecular(ISimulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>) - Constructor for class etomica.nbr.molecule.PotentialMasterNbrMolecular
potentialMasterRef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
potentialMasterRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
PotentialMasterSite - Class in etomica.nbr.site
PotentialMasterSite(ISimulation, int, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite: Invokes superclass constructor, specifying IteratorFactoryCell for generating molecule iterators.
PotentialMasterSite(ISimulation, BoxAgentManager.BoxAgentSource<BoxCellManager>, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite
PotentialMasterSite(ISimulation, BoxAgentManager.BoxAgentSource<BoxCellManager>, BoxAgentManager<BoxCellManager>, ISpace) - Constructor for class etomica.nbr.site.PotentialMasterSite
PotentialMasterSite(ISimulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>, AtomsetIteratorPDT) - Constructor for class etomica.nbr.site.PotentialMasterSite
PotentialMasterSite.BoxAgentSiteSource - Class in etomica.nbr.site
potentialMasterTarg - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
potentialMasterTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
potentialMasterTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
potentialMasterTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
potentialMasterTarget - Variable in class etomica.normalmode.SimOverlap
potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
potentialMCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
PotentialMEAM - Class in etomica.meam
PotentialMEAM(ISpace) - Constructor for class etomica.meam.PotentialMEAM
potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialMM - Variable in class etomica.zeolite.ZeoliteSimulation: The hard-sphere potential governing the interactions.
potentialMNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialMO - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
PotentialMolecular - Class in etomica.potential: Superclass for all Potential classes, which define how the atoms in the system interact with each other.
PotentialMolecular(int, ISpace) - Constructor for class etomica.potential.PotentialMolecular: General constructor for a potential instance
potentialMolecularInterNonBondedUnlike - Variable in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
PotentialMolecularMonatomic - Class in etomica.potential: Intermolecular potential that wraps an atomic potential.
PotentialMolecularMonatomic(ISpace, IPotentialAtomic) - Constructor for class etomica.potential.PotentialMolecularMonatomic
PotentialMolecularSoft - Interface in etomica.potential: Methods for properties obtained for a soft, differentiable pair potential.
PotentialMolecularSum - Class in etomica.potential: Molecular potential class that simply sums up contributions from multiple (molecular) potentials.
PotentialMolecularSum(IPotentialMolecular[]) - Constructor for class etomica.potential.PotentialMolecularSum
potentialN - Variable in class etomica.meam.EFSTungsten
potentialN - Variable in class etomica.meam.MEAM_3DMDwithGB
potentialN - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
potentialN - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
potentialN - Variable in class etomica.meam.MEAM_MC
potentialN - Variable in class etomica.meam.MEAMMd3D
PotentialN - Class in etomica.potential
PotentialN(ISpace) - Constructor for class etomica.potential.PotentialN: Constructor for PotentialN.
potentialN - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
potentialNN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialNN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialNO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialNO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
PotentialNonAdditive - Class in etomica.virial: Potential class which computes non-additive energies from potentials that return the full energies for various-sized groups of molecules.
PotentialNonAdditive(IPotentialMolecular[]) - Constructor for class etomica.virial.PotentialNonAdditive
PotentialNonAdditive(IPotentialMolecular[], int[]) - Constructor for class etomica.virial.PotentialNonAdditive
PotentialNonAdditive.PotentialNonAdditiveNB - Class in etomica.virial
PotentialNonAdditiveNB(int) - Constructor for class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
potentialOHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialOHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialOO - Variable in class etomica.modules.catalysis.Catalysis
potentialOO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
potentialOO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
potentialOS - Variable in class etomica.modules.catalysis.Catalysis
potentialPlus - Variable in class etomica.virial.MayerSphericalPlus
PotentialPolarizable - Interface in etomica.potential: Interface for a polarizable potential.
potentialQClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialQHCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialQHNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialQNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialQNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialQOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialQONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
PotentialReactive - Interface in etomica.potential: Interface for potentials that change the bond state of an atom.
PotentialReactive.BondChangeData - Class in etomica.potential
potentialRef - Variable in class etomica.virial.MayerPTAtt
potentialRef - Variable in class etomica.virial.MayerSphericalPTAtt
potentials - Variable in class etomica.virial.PotentialNonAdditive
potentialsAndIterators - Variable in class etomica.chem.models.Model
PotentialSoft - Interface in etomica.potential: Methods for properties obtained for a soft, differentiable pair potential.
potentialSpecies - Variable in class etomica.dimer.SimDimerMEAMadatom
potentialSpecies - Variable in class etomica.kmc.SimKMCMEAMadatom
potentialSW - Variable in class etomica.modules.insertion.InsertionGraphic
potentialSW - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
potentialSW - Variable in class etomica.modules.swmd.SwmdGraphic
potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosis
potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialThreaded - Variable in class etomica.threaded.atom.LJMD3DThreaded
potentialThreaded - Variable in class etomica.threaded.domain.LJMD3DThreaded
potentialThreaded - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
PotentialThreaded - Class in etomica.threaded
PotentialThreaded(ISpace, IPotentialAtomic[]) - Constructor for class etomica.threaded.PotentialThreaded
PotentialTruncated - Interface in etomica.potential: Interface for a potential that is artificially truncated, and thus which can provide a zero-body potential that (approximately) corrects for the truncation.
potentialwall - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potentialwall1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potentialwallPorousA - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potentialwallPorousA1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potentialwallPorousB - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potentialwallPorousB1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
potentialWater - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
potentialWrapper - Variable in class etomica.modules.colloid.ColloidSim
potentialWrapper - Variable in class etomica.modules.insertion.Insertion
potentialWrapper - Variable in class etomica.modules.pistoncylinder.PistonCylinder
potentialWrapper - Variable in class etomica.modules.swmd.Swmd
potentot(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
potentot(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
potparts(int, int, double, int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
potparts_old(int, int, double, int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
pots(double, double, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
pow - Variable in class etomica.data.DataPumpListenerPow
pow - Variable in class etomica.data.DataPumpListenerPowStrict
Pow - Class in etomica.graph.operations
Pow() - Constructor for class etomica.graph.operations.Pow
pow(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Power function.
pow(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Raise to a positive power.
pow(int) - Method in class etomica.veos.bigdecimal.Ifactor: Exponentiation with a positive integer.
pow(int) - Method in class etomica.veos.bigdecimal.Rational: Power to an integer.
pow(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Power to an integer.
pow(Rational) - Method in class etomica.veos.bigdecimal.Rational: Raise to a rational power.
pow - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
powerD(int) - Method in interface etomica.space.ISpace: Returns the given value raised to the Dth power, where D is the dimension of the space.
powerD(double) - Method in interface etomica.space.ISpace: Returns the given value raised to the Dth power, where D is the dimension of the space.
powerD(int) - Method in class etomica.space.Space
powerD(double) - Method in class etomica.space.Space
powerD(int) - Method in class etomica.space1d.Space1D
powerD(double) - Method in class etomica.space1d.Space1D
powerD(int) - Method in class etomica.space2d.Space2D
powerD(double) - Method in class etomica.space2d.Space2D
powerD(int) - Method in class etomica.space3d.Space3D
powerD(double) - Method in class etomica.space3d.Space3D
PowParameters - Class in etomica.graph.operations
PowParameters(byte) - Constructor for class etomica.graph.operations.PowParameters
powRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Raise to an integer power and round.
powRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Raise to an integer power and round.
powRound(BigDecimal, Rational) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Raise to a fractional power and round.
pPade - Variable in class etomica.util.numerical.VirialOptimizer
PREC - Static variable in class etomica.math.Gamma
prec2err(double, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Convert a precision (relative error) to an absolute error.
precalcQ - Variable in class etomica.virial.ClusterSumHS
precalcQ - Variable in class etomica.virial.ClusterWheatleyHS
precalcQ - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
precision - Variable in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
precision - Variable in class etomica.graphics.DeviceBox: Integer specifying the number of significant figures to be displayed.
precision - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
precision_s - Variable in class etomica.potential.EwaldSumMolecules
precisionLimit - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
PreconditionedConjugateGradient - Class in etomica.conjugategradient
PreconditionedConjugateGradient(Matrix, Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.PreconditionedConjugateGradient
PreconditionedConjugateGradientAlgorithm() - Method in class etomica.conjugategradient.PreconditionedConjugateGradient: Preconditioned Conjugate Gradient solution for Ax = b
predefinedArgbs - Static variable in class org.jmol.util.Colix
predefinedGroup1Names - Static variable in class org.jmol.viewer.JmolConstants
predefinedGroup3Names - Static variable in class org.jmol.viewer.JmolConstants
predefinedStatic - Static variable in class org.jmol.viewer.JmolConstants
predefinedVariable - Static variable in class org.jmol.viewer.JmolConstants
predictor() - Method in class etomica.integrator.IntegratorGear4
predictor() - Method in class etomica.integrator.IntegratorGear4NPH
Prefix - Class in etomica.units: Base class for all unit prefixes, such as kilo, micro, nano, etc.
prefix() - Method in class etomica.units.PrefixedUnit: Returns the prefix of the baseUnit.
prefixAllowed() - Method in class etomica.units.CompoundUnit
prefixAllowed() - Method in class etomica.units.PrefixedUnit: Returns false to indicate that a prefix cannot be applied to an already prefixed baseUnit.
prefixAllowed() - Method in class etomica.units.SimpleUnit: Returns flag indicating whether a prefix is allowed with this unit.
prefixAllowed() - Method in class etomica.units.systems.LJ.LJUnit
prefixAllowed() - Method in interface etomica.units.Unit: Indicates if the unit is appropriate for use with a prefix.
PrefixedUnit - Class in etomica.units: Implementation of the Unit interface formed from a base Unit (e.
PrefixedUnit(Unit) - Constructor for class etomica.units.PrefixedUnit: Constructs a PrefixedUnit using the given base and a Null prefix
PrefixedUnit(Prefix, Unit) - Constructor for class etomica.units.PrefixedUnit: Constructs a PrefixedUnit using the given prefix and base
preMultiply(Quaternion) - Method in class etomica.math.Quaternion: Returns the Quaternion r resulting from multiplying the input Quaternion preMultiplier to the current Quaternion q.
pRes - Variable in class etomica.normalmode.MeterSolidDA
preservestate - Static variable in class org.jmol.script.Token
press() - Method in class etomica.graphics.DeviceButton: Performs the button's action.
press() - Method in class etomica.zeolite.DeviceButtonSingle: Performs the button's action.
pressure - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
pressure - Variable in class etomica.association.MCMoveVolumeAssociated
pressure - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
pressure - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
pressure - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
pressure - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
pressure - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
pressure - Variable in class etomica.data.meter.MeterWidomInsertion
pressure - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
pressure - Variable in class etomica.integrator.mcmove.MCMoveVolume
pressure - Variable in class etomica.liquidLJ.MeterWidomInsertionP
pressure - Variable in class etomica.metastable.LJNPT.LJMCParams
pressure - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
pressure - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
pressure(double) - Method in class etomica.modules.adsorption.EOSSW
pressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
pressure - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
pressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
pressure - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
pressure - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
pressure - Variable in class etomica.normalmode.MCMoveVolumeSolid
pressure - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
pressure - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
pressure - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
pressure - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
pressure - Variable in class etomica.statmech.HardSphereSolid.EOSParams
Pressure - Class in etomica.units: Dimension for (3D) pressure.
pressure() - Method in class etomica.units.systems.CGS
pressure() - Method in class etomica.units.systems.LJ
pressure() - Method in class etomica.units.systems.MKS
pressure() - Method in class etomica.units.systems.UnitSystem
pressure() - Method in class etomica.units.systems.UnitSystem.Sim
pressure - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
pressure0 - Variable in class etomica.metastable.LJNPT.LJMCParams
Pressure2D - Class in etomica.units: Simulation unit of (2D) pressure is (D-A/ps^2)/A = D/ps^2
pressure2D() - Method in class etomica.units.systems.UnitSystem.Sim
pressureAverage - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
pressureDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
pressureFast - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
pressureFull - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
pressureHistory - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
pressureMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
pressureSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
pressureSliderPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
pressureTensor - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
pressureTensor - Variable in class etomica.integrator.IntegratorRigidIterative
pressureTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
pressureTensor - Variable in class etomica.integrator.IntegratorVelocityVerlet
pressureTensor - Variable in class etomica.integrator.IntegratorVerlet
pressureTensor - Variable in class etomica.modules.droplet.IntegratorDroplet
pressureTensor - Variable in class etomica.potential.PotentialCalculationForcePressureSum
pressureTensor - Variable in class etomica.potential.PotentialCalculationPressureTensor
pressureTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
pretendBox - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
pretendBox - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
pretendBox - Variable in class etomica.normalmode.MeterBoltzmannHTTP
pretendBox - Variable in class etomica.normalmode.MeterDDP
pretendBox - Variable in class etomica.normalmode.MeterDP
pretendBox - Variable in class etomica.normalmode.MeterTargetTP
prev - Variable in class etomica.lattice.IndexIteratorIncreasing
prev - Static variable in class org.jmol.script.Token
previous - Variable in class etomica.util.FunctionChain.Link
previous - Variable in class etomica.util.TreeLinker
previousTensor - Variable in class etomica.models.water.OrientationCalcWater3P
previousTensor - Variable in class etomica.models.water.OrientationCalcWater4P
previousValue - Variable in class etomica.normalmode.ModifierCells3D
previousValue - Variable in class etomica.normalmode.ModifierXCells2D
previousValue - Variable in class etomica.normalmode.ModifierYCells2D
prevprime(BigInteger) - Method in class etomica.veos.bigdecimal.Prime: return the largest prime smaller than n
pRigid - Variable in class etomica.potential.P2WaterPotentialsJankowski
primaryCoordDef - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
primaryCoordDef - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
Prime - Class in etomica.veos.bigdecimal: Prime numbers.
Prime() - Constructor for class etomica.veos.bigdecimal.Prime: Default constructor initializing a list of primes up to 17.
primeexp - Variable in class etomica.veos.bigdecimal.Ifactor
primitive - Variable in class etomica.lattice.BravaisLattice
Primitive - Class in etomica.lattice.crystal: Collection of primitive elements that specify or are determined by the structure of a Bravais lattice.
Primitive(ISpace) - Constructor for class etomica.lattice.crystal.Primitive: This constructor is called directly when a Primitive is constructing its reciprocal primitive.
primitive - Variable in class etomica.models.hexane.SimHarmonicHexane
primitive - Variable in class etomica.models.hexane.TestHexane
primitive - Variable in class etomica.models.hexane.TestHexaneFileConfig
primitive - Variable in class etomica.models.hexane.TestHexaneHarmonic
primitive - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
primitive - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
primitive - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
primitive - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
primitive - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
primitive - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
primitive - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
primitive - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
primitive - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
primitive - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
primitive - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
primitive - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
primitive - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
primitive - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
primitive - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage
primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
primitive - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
primitive - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
primitive - Variable in class etomica.models.oneDHardRods.SimWidomMode
primitive - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
primitive - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
primitive - Variable in class etomica.normalmode.CoordinateDefinition
primitive - Variable in class etomica.normalmode.HessianDB
primitive - Variable in class etomica.normalmode.LJVacancyMin
primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
primitive - Variable in class etomica.normalmode.NormalModes2D
primitive - Variable in class etomica.normalmode.NormalModes3D
primitive - Variable in class etomica.normalmode.NormalModesMolecular
primitive - Variable in class etomica.normalmode.SimBennet
primitive - Variable in class etomica.normalmode.SimCalcJ
primitive - Variable in class etomica.normalmode.SimCalcS
primitive - Variable in class etomica.normalmode.SimCalcSLJ
primitive - Variable in class etomica.normalmode.SimCalcSMorse
primitive - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
primitive - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
primitive - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
primitive - Variable in class etomica.normalmode.SimEinStep1
primitive - Variable in class etomica.normalmode.SimEinStep1HCP
primitive - Variable in class etomica.normalmode.SimEinStep2
primitive - Variable in class etomica.normalmode.SimEinStep2HCP
primitive - Variable in class etomica.normalmode.SimHarmonic
primitive - Variable in class etomica.normalmode.SimHarmonicUmbrella
primitive - Variable in class etomica.normalmode.SimLJHTTISuper
primitive - Variable in class etomica.normalmode.SimLJHTTISuperHCP
primitive - Variable in class etomica.normalmode.SimModesJ
primitive - Variable in class etomica.normalmode.SimOverlap
primitive - Variable in class etomica.normalmode.SimOverlapLJ
primitive - Variable in class etomica.normalmode.SimOverlapLJModule
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphere
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
primitive - Variable in class etomica.normalmode.SimOverlapSSnxy
primitive - Variable in class etomica.normalmode.SimTarget
primitive - Variable in class etomica.normalmode.SimTargetUmbrella
primitive - Variable in class etomica.normalmode.SimUmbrella
primitive - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
primitive - Variable in class etomica.normalmode.WaveVectorFactory2D
primitive - Variable in class etomica.normalmode.WaveVectorFactoryFcc
primitive - Variable in class etomica.normalmode.WaveVectorFactorySimple
primitive - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
primitive - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
primitive - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
PrimitiveBcc - Class in etomica.lattice.crystal: Primitive group for a body-centered-cubic system.
PrimitiveBcc(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveBcc
PrimitiveBcc(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveBcc
PrimitiveCubic - Class in etomica.lattice.crystal: Primitive group for a cubic system.
PrimitiveCubic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveCubic
PrimitiveCubic(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveCubic
PrimitiveFcc - Class in etomica.lattice.crystal: Primitive group for a face-centered-cubic system.
PrimitiveFcc(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveFcc
PrimitiveFcc(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveFcc
PrimitiveGeneral - Class in etomica.lattice.crystal: Primitive defined simply by its vectors.
PrimitiveGeneral(ISpace, IVector[]) - Constructor for class etomica.lattice.crystal.PrimitiveGeneral
PrimitiveHexagonal - Class in etomica.lattice.crystal: Primitive group for a hexagonal system.
PrimitiveHexagonal(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal
PrimitiveHexagonal(ISpace, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal
PrimitiveHexagonal.PrimitiveHexagonalReciprocal - Class in etomica.lattice.crystal
PrimitiveHexagonal2D - Class in etomica.lattice.crystal: Primitive group for a 2D hexagonal system.
PrimitiveHexagonal2D(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D
PrimitiveHexagonal2D(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D
PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal - Class in etomica.lattice.crystal
PrimitiveHexagonal2DReciprocal(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
PrimitiveHexagonalReciprocal(ISpace, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal.PrimitiveHexagonalReciprocal
PrimitiveHexane - Class in etomica.models.hexane: Implements the triclinic crystal structure derived from Dr.
PrimitiveHexane(ISpace) - Constructor for class etomica.models.hexane.PrimitiveHexane
PrimitiveMonoclinic - Class in etomica.lattice.crystal: Primitive group for a monoclinic system.
PrimitiveMonoclinic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic
PrimitiveMonoclinic(ISpace, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic
PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal - Class in etomica.lattice.crystal
PrimitiveMonoclinicReciprocal(ISpace, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
PrimitiveOrthorhombic - Class in etomica.lattice.crystal: Primitive group for an orthorhombic system.
PrimitiveOrthorhombic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombic
PrimitiveOrthorhombic(ISpace, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombic
PrimitiveOrthorhombicHexagonal - Class in etomica.lattice.crystal: Primitive group for an orthorhombic system.
PrimitiveOrthorhombicHexagonal(ISpace, double) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
PrimitiveTetragonal - Class in etomica.lattice.crystal: Primitive group for a tetragonal system.
PrimitiveTetragonal(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveTetragonal
PrimitiveTetragonal(ISpace, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTetragonal
PrimitiveTriclinic - Class in etomica.lattice.crystal: Primitive group for a triclinic system.
PrimitiveTriclinic(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveTriclinic
PrimitiveTriclinic(ISpace, double, double, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTriclinic
PrimitiveTrigonal - Class in etomica.lattice.crystal: Primitive group for a trigonal system.
PrimitiveTrigonal(ISpace) - Constructor for class etomica.lattice.crystal.PrimitiveTrigonal
PrimitiveTrigonal(ISpace, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTrigonal
primitiveUnitCell - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
primitiveUnitCell - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
primitiveUnitCell - Variable in class etomica.normalmode.HessianDB
primitiveUnitCell - Variable in class etomica.normalmode.SimCalcSLJ
primitiveUnitCell - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapLJ
primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphere
primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSSnxy
primitiveUnitCell - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
print(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
print - Variable in class etomica.potential.P2HydrogenHindePatkowski
print - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
print - Variable in class etomica.potential.P2HydrogenPatkowski
print - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
print() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
printapalooza - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
printInConvertedUnits - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
printInterval - Variable in class etomica.integrator.IntegratorRigidIterative
printInterval - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
printInterval - Variable in class etomica.integrator.IntegratorVelocityVerletShake
printInterval - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
printKeyAtomPositions() - Method in class etomica.action.IntegratorDimerApproach
printResults(double) - Method in class etomica.virial.simulations.SimulationVirial
printResults(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
printResults(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
printResults(double, String[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
printStrands(List, int) - Static method in class etomica.graph.property.FFTDecomposition
printStrands(List, int) - Static method in class etomica.graph.property.IsFFT
printStrands(List, int) - Static method in class etomica.virial.CalcFFT
printTargetHistogram() - Method in class etomica.virial.simulations.SimulationVirialOverlap2: Prints out the target histogram of maximum separation distances as set up by setupTargetHistogram().
probabilityBins - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
probabilityBins - Variable in class etomica.virial.MCMoveClusterTorsionMulti
probabilityReverseMap - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
probabilityReverseMap - Variable in class etomica.virial.MCMoveClusterTorsionMulti
probe - Static variable in class org.jmol.script.Token
proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController: Invoked when the rasterizer got an error while transcoding the input source.
proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in class etomica.graph.view.rasterizer.Main
proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in interface etomica.graph.view.rasterizer.SVGConverterController: Invoked when the rasterizer got an error while transcoding the input source.
proceedWithComputedTask(Transcoder, Map, List, List) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController: Invoked when the rasterizer has computed the exact description of what it should do.
proceedWithComputedTask(Transcoder, Map, List, List) - Method in class etomica.graph.view.rasterizer.Main
proceedWithComputedTask(Transcoder, Map, List, List) - Method in interface etomica.graph.view.rasterizer.SVGConverterController: Invoked when the rasterizer has computed the exact description of what it should do.
proceedWithSourceTranscoding(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController: Invoked when the rasterizer is about to start transcoding of a given source.
proceedWithSourceTranscoding(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.Main
proceedWithSourceTranscoding(SVGConverterSource, File) - Method in interface etomica.graph.view.rasterizer.SVGConverterController: Invoked when the rasterizer is about to start transcoding of a given source.
processAtoms(IAtomList) - Static method in class etomica.potential.P2WaterPotentialsJankowski
processData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLog
processData(IData) - Method in class etomica.data.DataAccumulator: Implementation of DataProcessor interface.
processData(IData) - Method in class etomica.data.DataGroupFilter: Returns the output data that was established with a previous call to processDataInfo.
processData(IData) - Method in class etomica.data.DataHistogram: Adds each value in the given Data to a single histogram.
processData(IData) - Method in class etomica.data.DataLogger: Gives data to DataSink for writing
processData(IData) - Method in class etomica.data.DataProcessor: Processes the input Data and returns Data for pushing to the next DataSink.
processData(IData) - Method in class etomica.data.DataProcessorChemicalPotential
processData(IData) - Method in class etomica.data.DataProcessorFunction: Applies the function to all elements of the input data.
processData(IData) - Method in class etomica.data.DataProcessorInterfacialTension
processData(IData) - Method in class etomica.data.DataPump: Returns the given Data.
processData(IData) - Method in class etomica.data.types.CastGroupOfTablesToDataTable: Converts data in given group to a DataDoubleArray as described in the general comments for this class.
processData(IData) - Method in class etomica.data.types.CastGroupToDoubleArray: Converts data in given group to a DataDoubleArray as described in the general comments for this class.
processData(IData) - Method in class etomica.data.types.CastToDouble: Extracts a double from the input data and returns it encapsulated in a DataDouble.
processData(IData) - Method in class etomica.data.types.CastToDoubleArray: Copies input Data to a DataDoubleArray and returns it (the DataDataDoubleArray).
processData(IData) - Method in class etomica.data.types.CastToGroup: Processes the input Data to update the output DataGroup.
processData(IData) - Method in class etomica.data.types.CastToTable: Copies input Data to a DataTable and returns it (the DataTable).
processData(IData) - Method in class etomica.densityofstate.DataProcessorPhi
processData(IData) - Method in class etomica.liquidLJ.DataProcessorReweight
processData(IData) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
processData(IData) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
processData(IData) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
processData(IData) - Method in class etomica.meam.DataProcessorCvMD
processData(IData) - Method in class etomica.metastable.DataProcessorXY
processData(IData) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
processData(IData) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
processData(IData) - Method in class etomica.modules.entropylottery.EntropyProcessor
processData(IData) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
processData(IData) - Method in class etomica.modules.interfacial.FitTanh
processData(IData) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
processData(IData) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBias
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorVar
processData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
processData(IData) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
processData(IData) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
processData(IData) - Method in class etomica.normalmode.BoltzmannProcessor
processData(IData) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
processData(IData) - Method in class etomica.normalmode.DataProcessorSum
processData(IData) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
processData(IData) - Method in class etomica.surfacetension.FitTanh
processData(IData) - Method in class etomica.surfacetension.SurfaceTensionMapped
processData(IData) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap: take in v1/pi1, pi0/pi1, spit out v1/pi, overlap0, overlap1, overlap2...
processData(IData) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
processData(IData) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverage: Prepares the accumulator for input data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlockless: Prepares the accumulator for input data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageCollapsingLog
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageCovariance
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixed: Prepares the accumulator for input data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixedOutputFile: Prepares the accumulator for input data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorCounter: Does nothing.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorHistogram: Sets up data and histograms, discarding any previous results.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorHistory: Sets up data and histories, discarding any previous results.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorRatioAverage
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorRatioAverageCovariance
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataGroupFilter: Determines data that will be output, using the given DataInfo and the index specification given at construction.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataHistogram: Sets up the histogram, discarding any previous results.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataLogger
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessor: Informs this DataProcessor of the DataInfo for the Data it will be processing.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorChemicalPotential
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorFunction: Returns a copy of the given dataInfo
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessorInterfacialTension
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataPump: Returns the given DataInfo.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastGroupOfTablesToDataTable: Prepares processor to handle Data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastGroupToDoubleArray: Prepares processor to handle Data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToDouble: Prepares processor to handle Data.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToDoubleArray: Prepares processor to perform cast.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToGroup
processDataInfo(IEtomicaDataInfo) - Method in class etomica.data.types.CastToTable: Prepares processor to perform cast.
processDataInfo(IEtomicaDataInfo) - Method in class etomica.densityofstate.DataProcessorPhi
processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweight
processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
processDataInfo(IEtomicaDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
processDataInfo(IEtomicaDataInfo) - Method in class etomica.meam.DataProcessorCvMD
processDataInfo(IEtomicaDataInfo) - Method in class etomica.metastable.DataProcessorXY
processDataInfo(IEtomicaDataInfo) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.entropylottery.EntropyProcessor
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.FitTanh
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBias
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorVar
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
processDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
processDataInfo(IEtomicaDataInfo) - Method in class etomica.normalmode.BoltzmannProcessor
processDataInfo(IEtomicaDataInfo) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
processDataInfo(IEtomicaDataInfo) - Method in class etomica.normalmode.DataProcessorSum
processDataInfo(IEtomicaDataInfo) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
processDataInfo(IEtomicaDataInfo) - Method in class etomica.surfacetension.FitTanh
processDataInfo(IEtomicaDataInfo) - Method in class etomica.surfacetension.SurfaceTensionMapped
processDataInfo(IEtomicaDataInfo) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
processDataInfo(IEtomicaDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
processDataInfo(IEtomicaDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
processReverseList() - Method in class etomica.integrator.IntegratorHard: Recalculate collision times (up) for any atoms atoms in the "reverse" list of atoms that thought they would collide with an atom that's changed.
product(ClusterDiagram, ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations: Returns a new cluster that is the product of the given clusters.
product(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Returns the product of all the given clusters.
product(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Returns an array of clusters formed from taking the product of each of the diagrams of the first set with each of the diagrams of the second set.
product(int[]) - Static method in class etomica.virial.cluster.Standard: Prepares a set of bond pairs for a clusters formed from a disconnected set of fully connected subclusters.
product3D(IVectorMutable, IVector, IVector) - Method in class etomica.potential.P2SpheroPolyhedron
profile1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
profile1pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
profile2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
profile2pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
profileData - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
profileDataInfo - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
profileDim - Variable in class etomica.data.meter.MeterProfile: Vector describing the orientation of the profile.
profileDim - Variable in class etomica.data.meter.MeterProfileByAtoms: Vector describing the orientation of the profile.
profileDim - Variable in class etomica.data.meter.MeterProfileByVolume: Vector describing the orientation of the profile.
profileDim - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
profilePlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
proj - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
proja - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
projb - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
projectOntoAxis(Point3f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
prompt(String, String, String[], boolean) - Method in interface org.jmol.api.ApiPlatform
prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
prop - Variable in class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
property - Variable in class etomica.graph.operations.SetPropertyFilter
Property - Interface in etomica.graph.property
property - Variable in class etomica.graphics.DeviceSlider: Property being modulated
property - Variable in class etomica.graphics.DeviceSpinner: Property being modulated
property - Variable in class etomica.modifier.ModifierGeneral
property - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
property - Variable in class etomica.virial.MeterVirialBinMultiThreaded
property - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
property - Static variable in class org.jmol.script.Token
PROPERTY_ALL - Static variable in class etomica.graph.operations.MaxIsomorph
propertyatomnumbercolumncount - Static variable in class org.jmol.script.Token
propertyatomnumberfield - Static variable in class org.jmol.script.Token
propertyChange(PropertyChangeEvent) - Method in class etomica.graphics.PropertyText: Listen to update display if editor changes value in some other way.
propertyChange(PropertyChangeEvent) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator: Called when a field's "value" property changes.
propertycolorscheme - Static variable in class org.jmol.script.Token
propertydatacolumncount - Static variable in class org.jmol.script.Token
propertydatafield - Static variable in class org.jmol.script.Token
PropertyFilter - Class in etomica.graph.iterators.filters
PropertyFilter(GraphIterator, Property) - Constructor for class etomica.graph.iterators.filters.PropertyFilter
propertyFilter - Variable in class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
PROPERTYFLAGS - Static variable in class org.jmol.script.Token
PropertyImpl - Class in etomica.graph.engine.impl
PropertyImpl(String) - Constructor for class etomica.graph.engine.impl.PropertyImpl
PropertyText - Class in etomica.graphics
PropertyText(PropertyEditor) - Constructor for class etomica.graphics.PropertyText
pRotConstraint - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
PRotConstraint - Class in etomica.models.nitrogen
PRotConstraint(ISpace, CoordinateDefinitionNitrogen, IBox) - Constructor for class etomica.models.nitrogen.PRotConstraint
pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
protein - Static variable in class org.jmol.script.Token
Psat - Variable in class etomica.interfacial.LJMD.LJMDParams
pSat() - Method in class etomica.modules.adsorption.EOSSW
psi(double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Digamma function.
psi - Static variable in class org.jmol.script.Token
pSimData - Variable in class etomica.util.numerical.B9Optimizer
pSimData - Variable in class etomica.util.numerical.VirialOptimizer
pSoluteMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
pSolutePM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
pSolutePP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
pSpan - Variable in class etomica.normalmode.MeterDDP
pSpan - Variable in class etomica.normalmode.MeterDP
pSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
pSplitter - Variable in class etomica.normalmode.DataSourceAvgPressure
pSplitter - Variable in class etomica.normalmode.DataSourceAvgPressure2
pSplitter - Variable in class etomica.normalmode.DataSourceMuRoot
pSplitter - Variable in class etomica.normalmode.DataSourceMuRoot1
pSplitter - Variable in class etomica.normalmode.DataSourceMuRootPMatch
pSplitter - Variable in class etomica.normalmode.DataSourcePMu
pSplitter - Variable in class etomica.normalmode.DataSourcePN
psuedoSinks - Variable in class etomica.data.DataSet
pSum - Variable in class etomica.normalmode.HSNPT.MyAgent
pSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
pSum2 - Variable in class etomica.normalmode.HSNPT.MyAgent
pSumXYZ - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
pSumXYZ1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
pSumXYZ1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
pSumXYZ2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
pSumXYZ2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
pt - Variable in class etomica.modules.materialfracture.MaterialFracture
pt - Variable in enum org.jmol.constant.EnumVdw
pt4Value(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
pThermalize - Variable in class etomica.modules.adsorption.P1Wall
pTmp - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
pTmp1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
pTmp1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
pTmp2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
pTmp2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
pTruncated - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
pTruncatedAA - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
pTruncatedAB - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
ptValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
pTW - Variable in class etomica.interfacial.LJMC
pTW - Variable in class etomica.interfacial.LJMD
pType - Variable in class etomica.models.nitrogen.SpeciesN2
pType - Variable in class etomica.models.nitrogen.SpeciesN2B
pType - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
pU - Variable in class etomica.virial.MayerENonGeneral
pullFactor - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
pump - Variable in class etomica.simulation.prototypes.LjMd3D
pump - Variable in class etomica.spin.Heisenberg
pump - Variable in class etomica.thermointegration.LjMc3D
pUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
pUnit - Variable in class etomica.modules.swmd.SwmdGraphic
purine - Static variable in class org.jmol.script.Token
PURPLE - Static variable in class org.jmol.util.Colix
pushInterval - Variable in class etomica.data.DataAccumulator: Accumulated data are pushed to the data sinks after every pushInterval calls
pushme - Static variable in class etomica.virial.ClusterWheatleySoft
pushme - Static variable in class etomica.virial.ClusterWheatleySoftBD
pushR2 - Variable in class etomica.virial.ClusterSumMultibody
pushR2 - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
pushR2 - Variable in class etomica.virial.ClusterSumPolarizable
pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
put(int, int) - Method in class org.jmol.util.Int2IntHash
put_rigid() - Method in class etomica.potential.P2WaterPotentialsJankowski
putCount - Variable in class etomica.data.DataAccumulator: Counter that keeps track of the number of interval events received since last call to updateSums
putData(IData) - Method in class etomica.data.DataArrayWriter
putData(IData) - Method in class etomica.data.DataDistributer
putData(IData) - Method in class etomica.data.DataDump
putData(IData) - Method in class etomica.data.DataFork: Puts the given Data through into all DataSinks.
putData(IData) - Method in class etomica.data.DataGroupSplitter
putData(IData) - Method in class etomica.data.DataLogger: Performs the open/write/close file actions in accordance with the settings of the Logger.
putData(IData) - Method in class etomica.data.DataProcessor: Processes input Data and pushes it downstream if output Data and DataSink are not null.
putData(IData) - Method in class etomica.data.DataSet.DataSetSink
putData(IData) - Method in class etomica.data.DataSinkConsole: Causes the given values to be written to the print stream.
putData(IData) - Method in class etomica.data.DataSplitter
putData(IData) - Method in class etomica.data.DataTableWriter
putData(IData) - Method in interface etomica.data.IDataSink: Gives data to DataSink for processing, display, or whatever it does.
putData(IData) - Method in class etomica.graphics.DisplayTextBox: Sets the display text to reflect the desired value from the datasource.
putData(IData) - Method in class etomica.graphics.DisplayTextBoxesCAE
putData(IData) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2: Add the given values to the sums and block sums
putData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim: Prepares the accumulator for input data.
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.AccumulatorAverageFixed
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataArrayWriter
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataDistributer
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataDump
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataFork: Puts the given DataInfo through into all DataSinks, inserting a data caster before any sinks needing one.
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataGroupSplitter
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataProcessor: Invokes processDataInfo on the given DataInfo, and passes the returned DataInfo to the dataSink (if not null).
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataSet.DataSetSink
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataSinkConsole: Causes the given DataInfo to be written to the print stream.
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataSplitter
putDataInfo(IEtomicaDataInfo) - Method in class etomica.data.DataTableWriter
putDataInfo(IEtomicaDataInfo) - Method in interface etomica.data.IDataSink: Informs the DataSink of the type of Data it should expect to receive.
putDataInfo(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayTextBox
putDataInfo(IEtomicaDataInfo) - Method in class etomica.graphics.DisplayTextBoxesCAE
putDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
putDataInfo(IEtomicaDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
putEdge(byte) - Method in interface etomica.graph.model.Graph
putEdge(byte, byte) - Method in interface etomica.graph.model.Graph
putEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
putEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
putValue(String, Object) - Method in class etomica.util.Grabber.ActionCornerSetter
pvBox - Variable in class etomica.modules.crystalviewer.LatticeEditor
pVirial - Variable in class etomica.util.numerical.B9Optimizer
pWater - Variable in class etomica.dielectric.TIP4P_NVT
pWertheim2Site - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
Pwr2 - Static variable in class org.jmol.util.TriangleData
PY - Static variable in class etomica.virial.cluster.ClusterOperations
PYGenerate(int, char) - Static method in class etomica.virial.PYGenerator: Returns the graphs (at each order, up to n+2) in the PY approximation to c.
PYGenerator - Class in etomica.virial
PYGenerator() - Constructor for class etomica.virial.PYGenerator
PYGenerator.IteratorEF - Class in etomica.virial
pyrimidine - Static variable in class org.jmol.script.Token
pythag(double, double) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal

Q

Q - Variable in class etomica.conjugategradient.ConjugateGradients
Q - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
Q - Variable in class etomica.conjugategradient.SteepestDescent
q - Variable in class etomica.mappedvirial.MappedUpotential
q - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
q - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
q - Variable in class etomica.models.co2.P2CO2Hellmann
q - Variable in class etomica.models.nitrogen.P2Nitrogen
Q - Variable in class etomica.potential.P2HePCKLJS
q - Variable in class etomica.potential.P2NitrogenHellmann
q - Variable in class etomica.potential.P3Induction.MyAgent
q - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
q0 - Variable in class etomica.math.Quaternion
q0 - Variable in class org.jmol.util.Quaternion
q1 - Variable in class etomica.math.Quaternion
q1 - Variable in class etomica.potential.P2Electrostatic
q1 - Variable in class etomica.potential.P2ElectrostaticWithHardCore
q1 - Variable in class org.jmol.util.Quaternion
q1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
q1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
q1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
q2 - Variable in class etomica.math.Quaternion
q2 - Variable in class etomica.potential.P2Electrostatic
q2 - Variable in class etomica.potential.P2ElectrostaticWithHardCore
q2 - Variable in class org.jmol.util.Quaternion
q2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
q2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
q3 - Variable in class etomica.math.Quaternion
q3 - Variable in class org.jmol.util.Quaternion
q3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
q4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
q_err - Variable in class etomica.potential.EwaldSumMolecules
qA - Static variable in class etomica.models.co2.P2CO2Hellmann
qA - Static variable in class etomica.potential.P2NitrogenHellmann
qA - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
qaa - Static variable in class etomica.potential.P2O2Bartolomei
qaaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
qaaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
qajmols - Static variable in class etomica.potential.P2O2Bartolomei
qajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
qajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
qajp1 - Static variable in class etomica.potential.P2O2Bartolomei
qajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
qajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
qajpn - Static variable in class etomica.potential.P2O2Bartolomei
qajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
qajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
qB - Static variable in class etomica.models.co2.P2CO2Hellmann
qB - Static variable in class etomica.potential.P2NitrogenHellmann
qB - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
qbet - Static variable in class etomica.potential.P2O2Bartolomei
qbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
qbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
qCalc(int, double[]) - Method in class etomica.veos.QSeries: Computes Q * N!/V^N based on the volume series for Q given by qCalc.
qCalc(double, int) - Method in class etomica.veos.Ushcats: Computes q, given as Q * N!/V^N, where Q is the configurational integral.
QFH - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
QFH - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
QFH - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
QFH - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
qH - Static variable in class etomica.models.water.P2WaterTIP4P
Qi - Variable in class etomica.normalmode.IntegratorHarmonic
qp - Variable in class etomica.mappedvirial.MappedUpotential
qp_q - Variable in class etomica.mappedvirial.MappedUpotential
qq - Variable in class etomica.potential.P2Electrostatic
qq - Variable in class etomica.potential.P2ElectrostaticWithHardCore
Qr - Variable in class etomica.normalmode.IntegratorHarmonic
QSeries - Class in etomica.veos: Fluid properties based on direct expansion of the canonical partition function Q in terms of irreducible cluster integrals beta.
QSeries(BetaSource) - Constructor for class etomica.veos.QSeries
qSite - Variable in class etomica.potential.P3Induction.MyAgent
qsqv - Variable in class etomica.potential.P2SpheroPolyhedron
qu - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
qu - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
quadId(int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams: Returns the quad ID for the given indices (id0, id1, id2, id3) and given number of molecules (n).
quadId(int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT: Returns the quad ID for the given indices (id0, id1, id2, id3) and given number of molecules (n).
Quadric - Class in org.jmol.util
Quadric(Vector3f[], float[], boolean) - Constructor for class org.jmol.util.Quadric
Quadric(double[]) - Constructor for class org.jmol.util.Quadric
quadStart - Static variable in class etomica.virial.cluster.VirialDiagrams
quadStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
quality - Variable in class etomica.graph.view.rasterizer.SVGConverter: Output image quality.
Quantity - Class in etomica.units: The dimension for the quantity of discrete things (e.g.
quantity() - Method in class etomica.units.systems.CGS
quantity() - Method in class etomica.units.systems.LJ
quantity() - Method in class etomica.units.systems.MKS
quantity() - Method in class etomica.units.systems.UnitSystem
quantity() - Method in class etomica.units.systems.UnitSystem.Sim
quat - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
quaternion - Variable in class etomica.atom.AtomOrientedQuaternion
Quaternion - Class in etomica.math: Quaternion object , its properties and associated operations
Quaternion(double[]) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q = p[0] + p[1]*i + p[2]*j + p[3]*k
Quaternion(double, IVectorMutable) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q = a + b
Quaternion(IVectorMutable, double) - Constructor for class etomica.math.Quaternion: Constructs the unit Quaternion q = cos(angle/2) + axis*sin(angle/2)
Quaternion(double, double, double, double) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q = a + b*i + c*j + d*k
Quaternion(double, double[]) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q = a + b[0]*i + b[1]*j + b[2]*k
Quaternion(OrientationFull3D) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q for an input OrientationFull3D with two vectors.
Quaternion(IVector[]) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q for an input basis vector array.
Quaternion(Matrix) - Constructor for class etomica.math.Quaternion: Constructs the Quaternion q given an input rotation matrix.
Quaternion - Class in org.jmol.util
Quaternion() - Constructor for class org.jmol.util.Quaternion
quaternionframe - Static variable in class org.jmol.script.Token
quatVelocity - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
quiet - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
quiet - Static variable in class etomica.virial.MeterVirialBinMultiThreaded
quiet - Static variable in class etomica.virial.MeterVirialEBinMultiThreaded
quintId(int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams: Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given number of molecules (n).
quintId(int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT: Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given number of molecules (n).
quintStart - Static variable in class etomica.virial.cluster.VirialDiagrams
quintStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
quit() - Method in interface etomica.graph.engine.ConsoleContainer
quit(Parser.Command) - Method in class etomica.graph.engine.Interpreter
quit() - Method in class etomica.graph.engine.Launcher.ConsoleWindow
quitSearch() - Method in class etomica.dimer.IntegratorDimerMin: Called after criteria is met in the rotateDimer method.

R

r - Variable in class etomica.action.IntegratorDimerApproach
r - Variable in class etomica.association.MCMoveVolumeAssociated
r - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
R - Variable in class etomica.conjugategradient.ConjugateGradients
R - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
R - Variable in class etomica.conjugategradient.SteepestDescent
r - Variable in class etomica.modules.rheology.ConformationPolymer
r - Variable in class etomica.modules.rheology.IntegratorPolymer
r - Variable in class etomica.modules.sam.P1Sinusoidal
r0 - Variable in class etomica.association.MCMoveDimerRotate
r0 - Variable in class etomica.association.MCMoveSmerRotate
r0 - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
r0 - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
r0 - Variable in class etomica.meam.ParameterSetMEAM
r0 - Variable in class etomica.meam.PotentialCuLREP
r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
R0 - Variable in class etomica.models.nitrogen.P2Nitrogen
R0 - Variable in class etomica.models.nitrogen.P2NitrogenAB
R0 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
R0 - Static variable in class etomica.models.water.P2WaterSzalewicz
r0 - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
r0 - Static variable in class etomica.potential.P2HydrogenHindePatkowski
r0 - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
r0 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
R0 - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
r0 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
r0 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
r00 - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
r01Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
r01Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
r02Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
r02Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
R1 - Variable in class etomica.meam.PotentialFeEAM_LS
R1 - Variable in class etomica.models.nitrogen.P2Nitrogen
R1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
R1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
r1 - Variable in class etomica.potential.P3HydrogenATM
r1 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
r1 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
r12 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
r12 - Variable in class etomica.potential.P3QChem.DampingParams
r12Vec - Variable in class etomica.potential.PotentialEmul
r12Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
r12Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
R2 - Variable in class etomica.meam.PotentialFeEAM_LS
r2 - Variable in class etomica.models.nitrogen.P2Nitrogen
r2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
r2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
r2 - Variable in class etomica.nbr.CriterionSimple
r2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
r2 - Variable in class etomica.potential.P3HydrogenATM
r2(Vector1D, Vector1D, IBoundary) - Static method in class etomica.space1d.Space1D: Computes the square of the magnitude of the difference of two vectors, subject to a nearest image transformation.
r2(Vector1D, Vector1D, IBoundary, Vector1D) - Static method in class etomica.space1d.Space1D: Computes the square of the magnitude of the difference of two vectors, subject to a nearest image transformation.
r2(Vector2D, Vector2D, IBoundary) - Static method in class etomica.space2d.Space2D: Computes the square of the magnitude of the difference of two vectors, subject to a nearest image transformation.
r2(Vector2D, Vector2D, IBoundary, Vector2D) - Static method in class etomica.space2d.Space2D: Computes the square of the magnitude of the difference of two vectors, subject to a nearest image transformation.
r2(Vector3D, Vector3D, IBoundary) - Static method in class etomica.space3d.Space3D: Computes the square of the magnitude of the difference of two vectors, subject to a nearest image transformation.
r2(Vector3D, Vector3D, IBoundary, Vector3D) - Static method in class etomica.space3d.Space3D: Computes the square of the magnitude of the difference of two vectors, subject to a nearest image transformation.
r2 - Variable in class etomica.virial.ClusterSumMultibody
r2 - Variable in class etomica.virial.ClusterWheatleyMultibody
r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
r2 - Variable in class etomica.virial.CoordinatePairLeafSet
r2 - Variable in class etomica.virial.CoordinatePairMoleculeSet
r2 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
r2 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
r2a - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
r2ab - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
r2b - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
r2Core - Variable in class etomica.potential.PotentialEmul
r2Cut - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
r2Cutoff - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
r2Cutoff - Variable in class etomica.potential.P2MoleculeTruncated
r2Cutoff - Variable in class etomica.potential.P2SoftSphericalTruncated
r2Cutoff - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
r2Cutoff - Variable in class etomica.potential.P2SoftTruncated
r2Cuts - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
r2Cuts - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
r2d2udr2 - Variable in class etomica.virial.PercusYevick1QC
r2Data - Variable in class etomica.potential.P2QChemInterpolated
r2MaxSafe - Variable in class etomica.nbr.CriterionSimple
r2MaxSafe - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
r2Switch - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
r2Switch - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
R3 - Variable in class etomica.meam.PotentialFeEAM_LS
r3 - Variable in class etomica.potential.P3HydrogenATM
rAB - Variable in class etomica.potential.EwaldSummation
rac - Variable in class etomica.dimer.P1LepsHarmonic
rAccum - Variable in class etomica.data.meter.MeterMeanSquareDisplacement
radau_f1_tst(IVectorMutable[]) - Method in class etomica.potential.P2WaterPotentialsJankowski
Radian - Class in etomica.units: Simulation unit for the measure of an angle.
radiansPerDegree - Static variable in class org.jmol.util.Measure
radiansPerDegree - Static variable in class org.jmol.viewer.JmolConstants
radicalColorMap - Variable in class etomica.modules.catalysis.ColorSchemeRadical
radicalColorMap - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
radioB - Variable in class etomica.modules.clustergenerator.MyApplet
radioB1 - Variable in class etomica.modules.clustergenerator.MyApplet
radius - Variable in class etomica.math.geometry.Hypersphere
radius - Static variable in class org.jmol.script.Token
random - Variable in class etomica.action.AtomActionRandomizeVelocity
random - Variable in class etomica.association.AtomSourceRandomDimer
random - Variable in class etomica.association.AtomSourceRandomSmer
random - Variable in class etomica.association.ColorSchemeSmer
random - Variable in class etomica.association.ColorSchemeSmerByLength
random - Variable in class etomica.association.MCMoveDimer
random - Variable in class etomica.association.MCMoveDimerRotate
random - Variable in class etomica.association.MCMoveSmer
random - Variable in class etomica.association.MCMoveSmerRotate
random - Variable in class etomica.association.MoleculeSourceRandomDimer
random - Variable in class etomica.atom.AtomSourceRandomLeaf
random - Variable in class etomica.atom.AtomSourceRandomSpecies
random - Variable in class etomica.atom.MoleculeSourceRandomMolecule
random - Variable in class etomica.box.RandomPositionSourceDeformable
random - Variable in class etomica.box.RandomPositionSourceRectangular
random - Variable in class etomica.data.AccumulatorAverageCollapsingLog
random - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
random - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
random - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
random - Variable in class etomica.integrator.IntegratorManagerMC
random - Variable in class etomica.integrator.IntegratorMC
random - Variable in class etomica.integrator.IntegratorMD: Elementary time step for the MD simulation
random - Variable in class etomica.integrator.mcmove.MCMoveAtom
random - Variable in class etomica.integrator.mcmove.MCMoveDimer
random - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
random - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
random - Variable in class etomica.integrator.mcmove.MCMoveMolecule
random - Variable in class etomica.integrator.mcmove.MCMoveVolume
random(int, int) - Static method in class etomica.math.linearalgebra.Matrix
random - Variable in class etomica.models.hexane.MCMoveCBMC
random - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
random - Variable in class etomica.models.hexane.MCMoveReptate
random - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
random - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
random - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
random - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
random - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
random - Variable in class etomica.models.nitrogen.MeterDirectInitPert
random - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
random - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
random - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
random - Variable in class etomica.modules.adsorption.P1Wall
random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
random - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
random - Variable in class etomica.modules.colloid.ConfigurationColloid
random - Variable in class etomica.modules.droplet.ConfigurationDroplet
random - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
random - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
random - Variable in class etomica.modules.rheology.ConformationPolymer
random - Variable in class etomica.normalmode.MCMoveAtomCoupled
random - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
random - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
random - Variable in class etomica.normalmode.MCMoveAtomSuperBox
random - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
random - Variable in class etomica.normalmode.MCMoveHarmonic
random - Variable in class etomica.normalmode.MCMoveHarmonicStep
random - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
random - Variable in class etomica.normalmode.MCMovePhaseAngle
random - Variable in class etomica.normalmode.MCMoveSingleMode
random - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
random - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
random - Variable in class etomica.normalmode.MCMoveWV
random - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
random - Variable in class etomica.simulation.Simulation
random - Variable in class etomica.spin.MCMoveSpinFlip
random - Variable in class etomica.util.numerical.AkimaSplineSmoother
random - Variable in class etomica.virial.cluster.ClusterDiagramTree
random - Variable in class etomica.virial.ClusterSumStickyEF
random - Variable in class etomica.virial.ConfigurationClusterAceticAcid
random - Variable in class etomica.virial.ConfigurationClusterMove
random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
random - Variable in class etomica.virial.MCMoveClusterAngleBend
random - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
random - Variable in class etomica.virial.MCMoveClusterReptateMulti
random - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
random - Variable in class etomica.virial.MCMoveClusterRingRegrow
random - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
random - Variable in class etomica.virial.MCMoveClusterRingScale
random - Variable in class etomica.virial.MeterVirialBDBin
random - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
random - Variable in class etomica.virial.MeterVirialBinMultiThreaded
random - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
random1 - Variable in class etomica.dimer.IntegratorDimerRT
randomAtom0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
randomAtom1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
randomDirection(IRandom) - Method in class etomica.space1d.Vector1D
randomizeDiagram() - Method in class etomica.virial.ClusterSumStickyEF: set the diagram used for calculating the value to a random one.
randomizeMomenta() - Method in class etomica.integrator.IntegratorHard: Updates collision times appropriately after randomizing momenta as part of the Andersen thermostat.
randomizeMomenta() - Method in class etomica.integrator.IntegratorMD: randomizes the velocities for the given box using velocities chosen form a Maxwell-Boltzmann distribution as in the Andersen thermostat.
randomizeMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
randomizeMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
randomizeMomenta() - Method in class etomica.integrator.IntegratorVerlet: Updates MrLast appropriately after randomizing momenta as part of the Andersen thermostat.
randomizeMomenta() - Method in class etomica.interfacial.IntegratorFixedWall
randomizeMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorHard: Updates collision time appropriately after randomizing momentum as part of the Andersen thermostat.
randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorMD: randomizes the velocity of an atom in the given box using velocities chosen form a Maxwell-Boltzmann distribution as in the Andersen thermostat.
randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorRigidIterative
randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorVerlet: Updates MrLast appropriately after randomizing momentum as part of the Andersen thermostat.
randomizeMomentum(IAtomKinetic) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
randomizePositions() - Method in class etomica.dimer.SimDimerLJadatom
randomizePositions() - Method in class etomica.kmc.IntegratorKMC
randomizePositions() - Method in class etomica.kmc.IntegratorKMCCluster
randomizePositions() - Method in class etomica.kmc.SimKMCLJadatom
randomizePositions() - Method in class etomica.kmc.SimKMCMEAMadatom
randomizer - Variable in class etomica.modules.adsorption.P1Wall
randomizeTotalKE() - Method in class etomica.integrator.IntegratorHard: Updates collision times appropriately after randomizing momenta as part of the Andersen scaling thermostat.
randomizeTotalKE() - Method in class etomica.integrator.IntegratorMD
randomLensPoint(IVector, IVector, Vector3D, IVectorMutable, double) - Method in class etomica.virial.MCMoveClusterAtomHSRing: Sets a given vector to a point chosen uniformly at random in the lens-shaped region formed by the overlap of two spheres of unit radius located at the given positions r1 and r2.
randomLensPoint(double, Vector3D) - Method in class etomica.virial.MCMoveClusterAtomHSRing: Returns a randomly selected point from within the lens-shaped region of overlap of two spheres of unit radius separated by a distance d.
randomLensPointInBox(IVector, IVector, IVectorRandom) - Method in class etomica.virial.MCMoveClusterAtomHSRing
RandomMersenneTwister - Class in etomica.util: Mersenne Twister RNG.
RandomMersenneTwister(int) - Constructor for class etomica.util.RandomMersenneTwister: Creates a Mersenne Twister with the given seed.
RandomMersenneTwister(int[]) - Constructor for class etomica.util.RandomMersenneTwister: Creates a Mersenne Twister with the given array of seeds.
randomMol0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
randomMol1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
randomNumber0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
randomNumber1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
RandomNumberGenerator - Class in etomica.util: Random number generator class.
RandomNumberGenerator() - Constructor for class etomica.util.RandomNumberGenerator
RandomNumberGenerator(long) - Constructor for class etomica.util.RandomNumberGenerator
RandomNumberGeneratorUnix - Class in etomica.util: Random number generator that takes random bits from files.
RandomNumberGeneratorUnix() - Constructor for class etomica.util.RandomNumberGeneratorUnix: Create an RNG using /dev/urandom as a source of random bits.
RandomNumberGeneratorUnix(String) - Constructor for class etomica.util.RandomNumberGeneratorUnix: Create an RNG using the given file as a source of random bits.
randomOrientation(IVectorMutable) - Method in class etomica.virial.MCMoveClusterPolyhedraChain
randomOrientation(IVectorMutable) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
randomPosition() - Method in interface etomica.box.RandomPositionSource: Returns a random position with the previously set box's boundary.
randomPosition() - Method in class etomica.box.RandomPositionSourceDeformable
randomPosition() - Method in class etomica.box.RandomPositionSourceRectangular
randomPosition() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
RandomPositionSource - Interface in etomica.box: Interface for an object which returns random positions within a box's boundary.
RandomPositionSourceDeformable - Class in etomica.box: Implementation of RandomPositionSource that can handle BoundaryDeformablePeriodic.
RandomPositionSourceDeformable(ISpace, IRandom) - Constructor for class etomica.box.RandomPositionSourceDeformable
RandomPositionSourceRectangular - Class in etomica.box
RandomPositionSourceRectangular(ISpace, IRandom) - Constructor for class etomica.box.RandomPositionSourceRectangular
randomRotation(IRandom, double) - Method in interface etomica.space.IOrientation: Perform a rotation by a random amount in the solid angle theta on the present orientation.
randomRotation(IRandom, double) - Method in class etomica.space2d.Orientation2D: Applies a random rotation of angle selected uniformly within plus or minus tStep from the current value.
randomRotation(IRandom, double) - Method in class etomica.space3d.Orientation3D: Applies a random rotation of angle selected uniformly from 0 to tStep.
randomRotation(IRandom, double) - Method in class etomica.space3d.OrientationFull3D: Applies a random rotation of angle selected uniformly from 0 to tStep.
randomSeeds - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
randomSeeds - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
randomSeeds - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
randomSeeds - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
range - Variable in class etomica.graphics.ColorSchemeTemperature
range - Variable in class etomica.lattice.RectangularLatticeNbrIteratorSquare
range - Variable in class etomica.modules.adsorption.MyMCMove
range - Variable in class etomica.modules.adsorption.P1Wall
range - Variable in class etomica.modules.colloid.P1Wall
range - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
range - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
range - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
range - Variable in class etomica.nbr.cell.NeighborCellManager
range - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
range - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
range - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
range - Variable in class etomica.nbr.list.PotentialMasterList
range - Static variable in class org.jmol.script.Token
RangeComparator() - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfined.RangeComparator
rangedAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
rangedAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
rangedAgentManager - Variable in class etomica.threaded.atom.PotentialMasterListWorker
rangedAgentManager - Variable in class etomica.threaded.domain.PotentialMasterListWorker
rangedPotentialIterator - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
rangedPotentialIterator - Variable in class etomica.nbr.PotentialMasterNbr
RangePermutator - Class in etomica.graph.iterators: This is a facility class that iterates through (maxP1 - minP1 + 1) permutations one at a time.
RangePermutator(int, int, int) - Constructor for class etomica.graph.iterators.RangePermutator
rangeselected - Static variable in class org.jmol.script.Token
rasmol - Static variable in class org.jmol.script.Token
RASTERIZER_SECURITY_POLICY - Static variable in class etomica.graph.view.rasterizer.Main: URL for Squiggle's security policy file
RATIO - Static variable in class etomica.data.AccumulatorRatioAverage
ratio - Variable in class etomica.data.AccumulatorRatioAverage
RATIO - Static variable in class etomica.data.AccumulatorRatioAverageCovariance
ratio - Variable in class etomica.data.AccumulatorRatioAverageCovariance
RATIO - Static variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
ratio - Variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
ratio - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
RATIO - Static variable in class etomica.overlap.DataOverlap
RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverage
RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverageCovariance
RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
RATIO_STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorRatioAverage
ratioError - Variable in class etomica.data.AccumulatorRatioAverage
ratioError - Variable in class etomica.data.AccumulatorRatioAverageCovariance
ratioError - Variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
ratioErrorStat - Variable in class etomica.virial.overlap.DataVirialOverlap
ratioMaxN - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
Rational - Class in etomica.util: Class handling rational numbers (numerator / denominator), including addition, multiplication and reducing (15/6 => 5/2).
Rational() - Constructor for class etomica.util.Rational
Rational(int, int) - Constructor for class etomica.util.Rational: Creates Rational instance with the given numerator and denominator.
Rational - Class in etomica.veos.bigdecimal: Fractions (rational numbers).
Rational() - Constructor for class etomica.veos.bigdecimal.Rational: Default ctor, which represents the zero.
Rational(BigInteger, BigInteger) - Constructor for class etomica.veos.bigdecimal.Rational: ctor from a numerator and denominator.
Rational(BigInteger) - Constructor for class etomica.veos.bigdecimal.Rational: ctor from a numerator.
Rational(int, int) - Constructor for class etomica.veos.bigdecimal.Rational: ctor from a numerator and denominator.
Rational(int) - Constructor for class etomica.veos.bigdecimal.Rational: ctor from an integer.
Rational(String) - Constructor for class etomica.veos.bigdecimal.Rational: ctor from a string representation.
Rational(String, int) - Constructor for class etomica.veos.bigdecimal.Rational: ctor from a string representation in a specified base.
ratios - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
ratioStandardDeviation - Variable in class etomica.data.AccumulatorRatioAverage
ratioStat - Variable in class etomica.virial.overlap.DataVirialOverlap
RAW_RGB - Static variable in class org.jmol.util.Colix
rawData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
rawData2 - Variable in class etomica.data.AccumulatorAverageCollapsingLog
rawData3 - Variable in class etomica.data.AccumulatorAverageCollapsingLog
rawDataBlockSize - Variable in class etomica.data.AccumulatorAverageCollapsingLog
RawDataWindowOpener(int, DisplayPlot) - Constructor for class etomica.graphics.DisplayPlot.RawDataWindowOpener
rBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
rBound(double, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: helper method that returns the position r if there are no bounds or if r is inside the bounds or (if r is outside the bounds) returns the position in the bounds nearest r.
rc - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
rc - Variable in class etomica.mappedvirial.MappedU.LJMDParams
rc - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
rc - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
rc - Variable in class etomica.metastable.LJmuVT.LJMCParams
rc - Variable in class etomica.metastable.LJNPT.LJMCParams
rc - Variable in class etomica.metastable.LJNVT.LJMCParams
rC - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
rC - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
rC - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
rC - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
rC - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
rC - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
rC - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
rC - Variable in class etomica.models.nitrogen.P2Nitrogen
rC - Variable in class etomica.models.nitrogen.P2NitrogenAB
rC - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
rC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
rc - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
rc - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
rc - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
rc - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
rc - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
rc - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimLJVacancy.LJParams
rc - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
rc - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
rc - Variable in class etomica.parser.ParserLAMMPS.Options
rc0 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
rc0 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
rC1 - Variable in class etomica.meam.PotentialCuLREP
rC1 - Variable in class etomica.meam.PotentialFeEAM
rC1 - Variable in class etomica.meam.PotentialFeEAM_LS
rC2 - Variable in class etomica.meam.PotentialCuLREP
rC2 - Variable in class etomica.meam.PotentialFeEAM
rC2 - Variable in class etomica.meam.PotentialFeEAM_LS
rCc - Variable in class etomica.meam.PotentialEFS
rCd - Variable in class etomica.meam.PotentialEFS
RcData - Variable in class etomica.potential.P2QChemInterpolated
rcLong - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
rcMax0 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
rcMax0 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
rcMax1 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
rcMax1 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
rcond - Static variable in class etomica.potential.P2WaterPotentialsJankowski
rcScale - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
rcScale - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
rcScale - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
rcShort - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
rcShort - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
rcShort - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
rCut - Variable in class etomica.models.water.P2Water4P
rCut - Variable in class etomica.potential.EwaldSumMolecules
rCut2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
rCut2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
rCut2 - Variable in class etomica.potential.Potential2SoftSphericalLS
rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibody
rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
rCutLJ - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
rCutLJ - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
rCutMax - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
rCutMax - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
rCutoff - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
rCutoff - Variable in class etomica.potential.P2MoleculeTruncated
rCutoff - Variable in class etomica.potential.P2SoftSphericalTruncated
rCutoff - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
rCutoff - Variable in class etomica.potential.P2SoftTruncated
rCutRealES - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
rCutRealES - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
rCutRealES - Variable in class etomica.potential.EwaldSummation
rCutSquared - Variable in class etomica.potential.EwaldSummation
rD - Variable in class etomica.data.meter.MeterPressureTensor
rData - Variable in class etomica.data.meter.MeterRDF
rData - Variable in class etomica.data.meter.MeterRDFPC
rData - Variable in class etomica.potential.P2QChemInterpolated
rdfdr - Variable in class etomica.virial.HypernettedChain
rdfdr - Variable in class etomica.virial.PercusYevick
rdfListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
rdfPump - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
rDistributionErrorHash - Variable in class etomica.virial.CalcFFT
rDistributionHash - Variable in class etomica.virial.CalcFFT
rdudr - Variable in class etomica.virial.PercusYevick1QC
re - Static variable in class etomica.potential.P1HydrogenMielke
ReactionEquilibrium - Class in etomica.modules.reactionequilibrium
ReactionEquilibrium() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibrium
ReactionEquilibriumGraphic - Class in etomica.modules.reactionequilibrium
ReactionEquilibriumGraphic(ReactionEquilibrium, ISpace) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
ReactionEquilibriumGraphic.Applet - Class in etomica.modules.reactionequilibrium
ReactionEquilibriumGraphic.MassEditor - Class in etomica.modules.reactionequilibrium
ReactionEquilibriumGraphic.MySpeciesEditor - Class in etomica.modules.reactionequilibrium
reactionField - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
reactionManagerCO - Variable in class etomica.modules.catalysis.Catalysis
ReactionManagerCO - Class in etomica.modules.catalysis
ReactionManagerCO(Catalysis) - Constructor for class etomica.modules.catalysis.ReactionManagerCO
read(String) - Method in interface etomica.graph.engine.ConsoleReader
read(String) - Method in class etomica.graph.engine.Interpreter
read(Parser.CommandVariableValue) - Method in class etomica.graph.engine.Interpreter
readData(String[]) - Method in class etomica.virial.MeterVirialBDBin
readData(String[]) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
readData(String[]) - Method in class etomica.virial.MeterVirialBinMultiThreaded
readData(String[], int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
readData(String[], int, boolean) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
readDataReBin(String[], int, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
readdb(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
readDistribution(int, boolean) - Method in class etomica.virial.CalcFFT
ReaderIn - Class in etomica.eigenstuff: Reads in a file.
ReaderIn() - Constructor for class etomica.eigenstuff.ReaderIn
readFile(String, double[][]) - Static method in class etomica.util.numerical.AkimaSplineSmootherApp
readFile(String, double[][]) - Static method in class etomica.util.numerical.AkimaSplineSmootherDyApp
readFile(String, double[][]) - Static method in class etomica.util.numerical.AkimaSplineSmootherMain
readLine(PipedInputStream) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
readMethod - Variable in class etomica.modifier.ModifierGeneral
readOutputFile() - Method in class etomica.potential.PotentialEmul
ReadParameters - Class in etomica.util: This class reads input parameters from a file and assigns the values to the fields of an object.
ReadParameters() - Constructor for class etomica.util.ReadParameters
ReadParameters(String) - Constructor for class etomica.util.ReadParameters
ReadParameters(String, ParameterBase) - Constructor for class etomica.util.ReadParameters
readParameters() - Method in class etomica.util.ReadParameters: Reads each line from inputFileName and attempts to match it with a field from parameterWrapper and sets the field to the value from the file.
readProcessData(String, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
readResolve() - Method in class etomica.graph.view.rasterizer.DestinationType
readWeights(String) - Method in class etomica.virial.MeterVirialBDBin
readWeights(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
readWeights(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
readWeights(String, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
readWriteData(String[], String, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded: This method reads all input files in parallel and writes lines out to the new file as the bin data is known to be complete.
ready - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
real() - Method in class etomica.math.Complex: Real part of this Complex number, the x-coordinate in rectangular coordinates.return Re[z] where z is this Complex number.
REAL - Static variable in class etomica.util.Transform.Fourier
realT - Variable in class etomica.normalmode.MeterHarmonicCoordinate
realT - Variable in class etomica.normalmode.MeterHarmonicEnergy
realT - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
realT - Variable in class etomica.normalmode.MeterNormalMode
realYm(int, int, double, double) - Static method in class etomica.math.SphericalHarmonics
reblockData() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Reblock data from rawData2 into rawData3, then copy it back to rawData2
reblockData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog: Reblock data from rawData into rawData2, taking blocks of size n
rebuild(Object) - Method in interface etomica.util.DirtyObject
Reciprocal() - Constructor for class etomica.util.Function.Reciprocal
reclaim(IAtom) - Method in class etomica.association.ColorSchemeSmer
recomputeColumnHeaders() - Method in class etomica.graphics.DisplayTable: Reconstruct the column headers array.
recomputeCriteriaRanges() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Recomputes the range for all criterion based on our own range.
recomputeCriteriaRanges() - Method in class etomica.nbr.list.PotentialMasterList: Recomputes the range for all criterion based on our own range.
recomputeMoveFrequencies() - Method in class etomica.integrator.mcmove.MCMoveManager: Recomputes all the move frequencies.
recomputeUnits() - Method in class etomica.graphics.DisplayTable: Reconstruct the units array.
recomputeWeights() - Method in class etomica.virial.MeterVirialBDBin
recomputeWeights() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long, boolean) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded: This method will read MyData.unscreenedCount and MyData.accumulator and write to MyData.weight.
recomputeWeights() - Method in class etomica.virial.MeterVirialBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long, boolean) - Static method in class etomica.virial.MeterVirialBinMultiThreaded: This method will read MyData.unscreenedCount and MyData.accumulator and write to MyData.weight.
recomputeWeights() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, boolean, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded: This method will read MyData.unscreenedCount and MyData.accumulator and write to MyData.weight.
reconfig - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
reconfig - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
Rectangle - Class in etomica.math.geometry: A 2-dimensional geometric rectangle.
Rectangle(ISpace) - Constructor for class etomica.math.geometry.Rectangle: Constructs a square rectangle of unit size.
Rectangle(ISpace, double, double) - Constructor for class etomica.math.geometry.Rectangle: Constructs a rectangle with edge lengths having the given values.
RECTANGLE - Static variable in class g3dsys.control.G3DSys
RectangleOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
Rectangular - Interface in etomica.math.geometry: Interface for a polytope with shape that can be specified by the length of D sides.
RectangularLattice - Class in etomica.lattice: Basic implementation of the AbstractLattice interface, providing construction and access of sites for a lattice of arbitrary dimension.
RectangularLattice(int, SiteFactory) - Constructor for class etomica.lattice.RectangularLattice: Constructs a lattice of the given dimension (D) with sites made from the given factory.
RectangularLattice.Iterator - Class in etomica.lattice: Iterates over all sites of the lattice.
RectangularLatticeNbrIterator - Class in etomica.lattice: An abstract iterator that generates the neighboring sites of a given site.
RectangularLatticeNbrIterator(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIterator: Constructs iterator that needs to be configured before use.
RectangularLatticeNbrIteratorAdjacent - Class in etomica.lattice: Iterates over the neighbors of a site, where neighbors are those sites immediately adjacent to it in each direction; this does not include sites diagonal to the site.
RectangularLatticeNbrIteratorAdjacent(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIteratorAdjacent
RectangularLatticeNbrIteratorSquare - Class in etomica.lattice: Iterates over neighbors of a site, where neighbors are defined as those sites lying in a rectangular region centered on the site.
RectangularLatticeNbrIteratorSquare(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIteratorSquare
recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
recursiveTag(IAtom) - Method in class etomica.modules.chainequilibrium.MeterChainLength
RED - Static variable in class org.jmol.util.Colix
redColorScheme - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
redistributeForces(IMolecule, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Method in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
redomove - Static variable in class org.jmol.script.Token
reduce(long, long) - Method in class etomica.graph.model.impl.CoefficientImpl
reduce(ArrayList<ClusterDiagram>) - Static method in class etomica.virial.cluster.ClusterOperations: Sorts cluster diagrams (but # of connections) and combines any diagrams that are identical, resulting in a diagram with a weight equal to the sum of the original weights.
reducedTemp - Variable in class etomica.virial.CalcFFT
ReeHoover - Class in etomica.graph.operations: This operation performs conversion from a set of biconnected graphs with f edges to a set of diagrams of fully connected diagrams with e and f edges.
ReeHoover() - Constructor for class etomica.graph.operations.ReeHoover
ReeHoover.ReeHooverParameters - Class in etomica.graph.operations
reeHooverCB - Variable in class etomica.modules.clustergenerator.MyApplet
ReeHooverMC - Class in etomica.virial.simulations: An implementation of MSMC with direct sampling for computation of virial coefficients of hard spheres, in the spirit of Ree-Hoover Monte Carlo (Ree & Hoover, 1964, Fifth and Sixth Virial Coefficients for Hard Spheres and Hard Disks).
ReeHooverMC() - Constructor for class etomica.virial.simulations.ReeHooverMC
ReeHooverMC.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
ReeHooverParameters(char) - Constructor for class etomica.graph.operations.ReeHoover.ReeHooverParameters
ReeHooverToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
ref - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
REF - Static variable in class etomica.overlap.DataOverlap
ref - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
ref - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
ref - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
ref - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
ref - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
ref - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
refAccumulator - Variable in class etomica.virial.overlap.DataSourceVirialOverlap
refAccumulator - Variable in class etomica.virial.overlap.DataVirialOverlap
refAvg - Variable in class etomica.overlap.DataOverlap
refAvg - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
reference - Variable in class etomica.compatibility.FeatureRequirement
referenceDataInterval - Variable in class etomica.normalmode.SimOverlapModule
refErr - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
refFrac - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
refFrac - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
refFrac - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
refFrac - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
refFrac - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
refFrac - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
refFrac - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
refFrac - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
refFrac - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
refFrac - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
refFrac - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
refFrac - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
refFrac - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
refFrac - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
refFrac - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
refFrac - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
refFrac - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
refFrac - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
refFrac - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
refFrac - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
refFrac - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
refFrac - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
refFrac - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
refFrac - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
refFrac - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
refFrac - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
refFrac - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
refFrac - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
refFrac - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
refFrac - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
refFrac - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
refFrac - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
refFrac - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
refFrac - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
refFrac - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
refFrac - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
refFreq - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
refFreq - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
refFreq - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
refFreq - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
refFreq - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
reflect() - Method in class etomica.normalmode.MeterSolidMirror
refPref - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
refPref - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
refPref - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
refPref - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
refPref - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
refPref - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
refPref - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
refPref - Variable in class etomica.normalmode.MeterSamplingHarmonic
refPref - Variable in class etomica.normalmode.MeterSamplingTarget
refPref - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
refPref - Variable in class etomica.normalmode.MeterWorkBennetTarget
refPref - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
refPref - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
refPref - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
refPref - Variable in class etomica.normalmode.MeterWorkTargetBennet
refPref - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
refPref - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
refPref - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
refPref - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
refPref - Variable in class etomica.normalmode.SimBennet
refPref - Variable in class etomica.normalmode.SimHarmonicUmbrella
refPref - Variable in class etomica.normalmode.SimOverlap
refPref - Variable in class etomica.normalmode.SimOverlapLJ
refPref - Variable in class etomica.normalmode.SimOverlapLJModule
refPref - Variable in class etomica.normalmode.SimOverlapSoftSphere
refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
refPref - Variable in class etomica.normalmode.SimOverlapSSnxy
refPref - Variable in class etomica.normalmode.SimTargetUmbrella
refPref - Variable in class etomica.normalmode.SimUmbrella
refPref - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
refPref - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
refPref - Variable in class etomica.virial.simulations.SimulationVirialOverlap
refPref - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
refPrefFileName - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
refPrefFileName - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
refPrefFileName - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
refresh() - Method in class etomica.graphics.DevicePlotPoints: Instructs the plot to redisplay any plotted functions with the most recent data.
refresh() - Method in class g3dsys.control.G3DSys: For a thorough redraw of the display
refreshAtomAgentMgr() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: refreshAtomAgentMgr() - sets the new atom manager based upon the box.
refreshing - Static variable in class org.jmol.script.Token
refreshSize() - Method in class etomica.graphics.DisplayBoxCanvas1D
refreshSize() - Method in class etomica.graphics.DisplayBoxCanvas2D
refreshSize() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
refSum - Variable in class etomica.normalmode.MeterOverlapSwitch
rejectNotify() - Method in class etomica.association.MCMoveBiasUB
rejectNotify() - Method in class etomica.association.MCMoveBiasUBMolecule
rejectNotify() - Method in class etomica.association.MCMoveDimer: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.association.MCMoveDimerRotate: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.association.MCMoveRotateAssociated
rejectNotify() - Method in class etomica.association.MCMoveSmer: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.association.MCMoveSmerRotate: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.association.MCMoveVolumeAssociated
rejectNotify() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
rejectNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
rejectNotify() - Method in class etomica.integrator.mcmove.MCMove: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveAtom: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveDimer: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveMolecule
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveRotate
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration: Performs no action; nothing required when move rejected.
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveVolume
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
rejectNotify() - Method in class etomica.interfacial.MCMoveAtomNbr
rejectNotify() - Method in class etomica.models.hexane.MCMoveCBMC
rejectNotify() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
rejectNotify() - Method in class etomica.models.hexane.MCMoveReptate
rejectNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
rejectNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
rejectNotify() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
rejectNotify() - Method in class etomica.modules.adsorption.MyMCMove
rejectNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupled: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.normalmode.MCMoveAtomSuperBox: Method called by IntegratorMC in the event that the most recent trial move is rejected.
rejectNotify() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
rejectNotify() - Method in class etomica.normalmode.MCMoveHarmonic
rejectNotify() - Method in class etomica.normalmode.MCMoveHarmonicStep
rejectNotify() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
rejectNotify() - Method in class etomica.normalmode.MCMovePhaseAngle
rejectNotify() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
rejectNotify() - Method in class etomica.normalmode.MCMoveSingleMode
rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolid
rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
rejectNotify() - Method in class etomica.normalmode.MCMoveWV
rejectNotify() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
rejectNotify() - Method in class etomica.spin.MCMoveSpinFlip
rejectNotify() - Method in class etomica.virial.BoxCluster: Informs the box that the trial was rejected so it will go back to the old coordinate pairs.
rejectNotify() - Method in class etomica.virial.MCMoveChangeBondLength
rejectNotify() - Method in class etomica.virial.MCMoveClusterAngleBend
rejectNotify() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtom
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSChain
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSRing
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSTree
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomMulti
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomQ
rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
rejectNotify() - Method in class etomica.virial.MCMoveClusterDiagram
rejectNotify() - Method in class etomica.virial.MCMoveClusterMolecule
rejectNotify() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
rejectNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
rejectNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
rejectNotify() - Method in class etomica.virial.MCMoveClusterReptateMulti
rejectNotify() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrow
rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
rejectNotify() - Method in class etomica.virial.MCMoveClusterRingScale
rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateCH3
rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionMulti
rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleMulti
rejectNotify() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
Relabel - Class in etomica.graph.operations
Relabel() - Constructor for class etomica.graph.operations.Relabel
relabel - Variable in class etomica.graph.property.FFTDecomposition
relabel - Variable in class etomica.graph.property.IsFFT
relabel(Graph) - Static method in class etomica.virial.IEGenerator
RelabelParameters - Class in etomica.graph.operations
RelabelParameters(byte[]) - Constructor for class etomica.graph.operations.RelabelParameters
RelabelWertheim - Class in etomica.graph.operations
RelabelWertheim() - Constructor for class etomica.graph.operations.RelabelWertheim
relax() - Method in class etomica.space3d.OrientationFull3D: Normalizes both direction and secondaryDirection
relaxAction - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
relaxInterval - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
relaxMolecule(IMolecule) - Method in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
releaseAgent(AtomArrayList, IAtom, IBox) - Method in class etomica.association.AssociationManager
releaseAgent(Object, IMolecule) - Method in class etomica.association.AssociationManagerMolecule
releaseAgent(ColorSchemeSmer.ColorAgent, IAtom, IBox) - Method in class etomica.association.ColorSchemeSmer
releaseAgent(MCMoveVolumeAssociated.Agent, IAtom, IBox) - Method in class etomica.association.MCMoveVolumeAssociated
releaseAgent(Object, IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
releaseAgent(E, IAtom, IBox) - Method in interface etomica.atom.AtomLeafAgentManager.AgentSource: This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
releaseAgent(Object, IAtomType) - Method in interface etomica.atom.AtomTypeAgentManager.AgentSource: This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
releaseAgent(Object, IAtomType) - Method in class etomica.atom.DiameterHashByType
releaseAgent(Object, IMolecule) - Method in interface etomica.atom.MoleculeAgentManager.MoleculeAgentSource: This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
releaseAgent(Object, ISpecies) - Method in interface etomica.atom.SpeciesAgentManager.AgentSource: This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements.
releaseAgent(E) - Method in interface etomica.box.BoxAgentManager.BoxAgentSource
releaseAgent(AtomLeafAgentManager<E>) - Method in class etomica.box.BoxAgentSourceAtomManager
releaseAgent(MoleculeAgentManager) - Method in class etomica.box.BoxAgentSourceMoleculeManager
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
releaseAgent(Object, IMolecule) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.dimer.IntegratorDimerMin
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.dimer.IntegratorDimerRT
releaseAgent(Object, IAtom, IBox) - Method in class etomica.dimer.IntegratorEnergyMap
releaseAgent(ArrayList, IAtom, IBox) - Method in class etomica.graphics.BondListener
releaseAgent(Object, IAtomType) - Method in class etomica.graphics.ColorSchemeByType
releaseAgent(Color, IAtom, IBox) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
releaseAgent(Color, IAtom, IBox) - Method in class etomica.graphics.ColorSchemeRandom
releaseAgent(Object, IMolecule) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
releaseAgent(Ball[], IAtom, IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
releaseAgent(Figure, IAtom, IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
releaseAgent(IntegratorConNVT.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorConNVT
releaseAgent(IntegratorGear4.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorGear4
releaseAgent(IntegratorHard.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorHard
releaseAgent(Object, IAtomType) - Method in class etomica.integrator.IntegratorHard
releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.integrator.IntegratorMD.VectorSource
releaseAgent(Object, IMolecule) - Method in class etomica.integrator.IntegratorRigidIterative
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorRigidIterative
releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorRigidIterative
releaseAgent(IntegratorRigidMatrixIterative.AtomAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
releaseAgent(Object, IMolecule) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorVelocityVerlet
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.integrator.IntegratorVelocityVerletShake
releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
releaseAgent(IntegratorVerlet.Agent, IAtom, IBox) - Method in class etomica.integrator.IntegratorVerlet
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedU
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedVirial
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMappedVirialV
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.mappedvirial.MeterMeanForce
releaseAgent(EwaldSummation.MyCharge, IAtom, IBox) - Method in class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
releaseAgent(Object, IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
releaseAgent(Object, IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
releaseAgent(EwaldSummation.MyCharge, IAtom, IBox) - Method in class etomica.models.water.ChargeAgentSourceTIP4PWater
releaseAgent(InteractionTracker.CatalysisAgent, IAtom, IBox) - Method in class etomica.modules.catalysis.InteractionTracker
releaseAgent(AtomFilterChainLength.LengthAgent, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
releaseAgent(IAtom[], IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
releaseAgent(ColorSchemeRadical.LengthAgent, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
releaseAgent(Object, IAtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
releaseAgent(IAtom[], IAtom, IBox) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
releaseAgent(MeterChainLength.AtomTag, IAtom, IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
releaseAgent(Boolean, IAtom, IBox) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
releaseAgent(IntegratorDroplet.MyAgent, IAtom, IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
releaseAgent(IAtom, IAtom, IBox) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
releaseAgent(Object, IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.modules.rosmosis.P1Tether
releaseAgent(Object, IMolecule) - Method in class etomica.modules.sam.CriterionTether3
releaseAgent(NeighborCellManager) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
releaseAgent(NeighborCellManagerMolecular) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
releaseAgent(Object, IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Removes the given atom from the cell.
releaseAgent(Cell, IAtom, IBox) - Method in class etomica.nbr.cell.NeighborCellManager: Removes the given atom from the cell.
releaseAgent(CriterionPositionWall.DoubleWrapper, IAtom, IBox) - Method in class etomica.nbr.CriterionPositionWall
releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.nbr.CriterionSimple
releaseAgent(Object, IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
releaseAgent(Object, IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
releaseAgent(NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
releaseAgent(AtomPotentialList, IAtom, IBox) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
releaseAgent(AtomNeighborLists, IAtom, IBox) - Method in class etomica.nbr.list.NeighborListManager
releaseAgent(NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
releaseAgent(Object, IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
releaseAgent(Object, ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
releaseAgent(Object, IAtomType) - Method in class etomica.nbr.PotentialMasterNbr
releaseAgent(Object, ISpecies) - Method in class etomica.nbr.PotentialMasterNbr
releaseAgent(AtomSite, IAtom, IBox) - Method in class etomica.nbr.site.NeighborSiteManager
releaseAgent(BoxCellManager) - Method in class etomica.nbr.site.PotentialMasterSite.BoxAgentSiteSource
releaseAgent(IVectorMutable, IAtom, IBox) - Method in class etomica.normalmode.CoordinateDefinition.SiteSource
releaseAgent(Object, IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
releaseAgent(Object, IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
releaseAgent(HSNPT.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.HSNPT.ActionSummer
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.MeterDADB
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.MeterSolidProps
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.normalmode.MeterSolidPropsLJ
releaseAgent(Object, IAtom, IBox) - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
releaseAgent(Object, IMolecule) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
releaseAgent(P2HardBondedList.BondArrayList, IAtom, IBox) - Method in class etomica.potential.P2HardBondedList
releaseAgent(AtomArrayList, IAtom, IBox) - Method in class etomica.potential.P2SquareWellRobust
releaseAgent(Object, IAtomType) - Method in class etomica.potential.PotentialMasterMonatomic
releaseAgent(IntegratorVelocityVerletQuaternion.AtomAgent, IAtom, IBox) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
releaseAgent(Object, IMolecule) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
releaseAgent(Object, ISpecies) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
releaseAgent(Integrator.Forcible, IAtom, IBox) - Method in class etomica.surfacetension.SurfaceTensionMapped
releaseAgent(NeighborCellManagerThreaded) - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, IBox) - Method in class etomica.util.numerical.CalcGradientDifferentiable
releaseBond(Object) - Method in interface etomica.graphics.BondManager: Notifies the BondManager that the given bond no longer exists in the system.
releaseBond(Object) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Removes the given bond from the graphical display.
releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
releaseScreenImage() - Method in class org.jmol.util.GData
remove(int) - Method in class etomica.atom.AtomArrayList: This removes the atom at the given index and shifts the remaining atoms back (maintaining the order).
remove(int) - Method in class etomica.atom.MoleculeArrayList
remove() - Method in class etomica.graph.iterators.CartesianIterator
remove() - Method in class etomica.graph.iterators.CartesianPermutator
remove() - Method in class etomica.graph.iterators.ChainedIterator
remove() - Method in class etomica.graph.iterators.DefaultIterator
remove() - Method in class etomica.graph.iterators.DefaultPermutator
remove() - Method in class etomica.graph.iterators.EdgelessIterator
remove() - Method in class etomica.graph.iterators.filters.GlobalFilter
remove() - Method in class etomica.graph.iterators.filters.LocalFilter
remove() - Method in class etomica.graph.iterators.FixedEdgeCountIterator
remove() - Method in class etomica.graph.iterators.IteratorWrapper
remove() - Method in class etomica.graph.iterators.RangePermutator
remove() - Method in class etomica.graph.iterators.StoredIterator
remove(Object) - Method in class etomica.graph.model.GraphList
remove(Display) - Method in class etomica.graphics.SimulationGraphic
remove(Device) - Method in class etomica.graphics.SimulationGraphic
remove(int) - Method in class etomica.potential.P2HardBondedList.BondArrayList
remove(IFunction) - Method in class etomica.util.FunctionChain: Removes the given function from the chain.
remove(int) - Method in class etomica.util.ObjectArrayList: Removes the element at the specified position in this list.
remove() - Method in class etomica.util.TreeLinker: Disconnects this linker from the linkers above and below it, and puts them in sequence, repairing the hole.
remove(TreeLinker) - Static method in class etomica.util.TreeList
remove() - Method in class etomica.virial.PYGenerator.IteratorEF
removeAction(IAction) - Method in interface etomica.action.ActionGroup: Removes the given oldAction from the group.
removeAction(IAction) - Method in class etomica.action.ActionGroupSeries: Removes the given action from the group.
removeAction(IAction) - Method in class etomica.action.activity.ActivityGroupParallel
removeAction(IAction) - Method in class etomica.action.activity.ActivityGroupSeries: Removes the given action from the list of actions performed by this controller.
removeAction(IAction) - Method in class etomica.action.activity.Controller
removeAll(Collection<?>) - Method in class etomica.graph.model.GraphList
removeAllValueChangedListeners() - Method in class etomica.graphics.DeviceBox: Removes all objects that are listening for a value changed event.
removeAndReplace(int) - Method in class etomica.atom.AtomArrayList: This removes the atom at the given index and replaces the hole with the last atom.
removeAndReplace(int) - Method in class etomica.atom.MoleculeArrayList
removeAtom(IAtom) - Method in class etomica.nbr.cell.Cell
removeAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerLJadatom
removeAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMadatom
removeAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMGB
removeAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCLJadatom
removeAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCMEAMadatom
removeBox(IBox) - Method in interface etomica.api.ISimulation: Removes a Box to the simulation.
removeBox(IBox) - Method in class etomica.simulation.Simulation
removeChildAtom(IAtom) - Method in class etomica.atom.Molecule: Removes the given child Atom from this AtomGroup.
removeChildType(IAtomType) - Method in class etomica.species.Species
removeChildType(IAtomType) - Method in class etomica.species.SpeciesSpheresHetero: Removes the given factory as a child of this factory.
removeCollisionListener(IntegratorHard.CollisionListener) - Method in class etomica.integrator.IntegratorHard: De-registers an object from the list of collision listeners.
removeCountOfSpeciesSLMListener(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removeData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
removeData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
removeData() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
removeDataListener(DataSetListener) - Method in class etomica.data.DataSet
removeDataSink(IDataSink) - Method in class etomica.data.DataFork
removeDataSink(IDataSink) - Method in interface etomica.data.DataPipeForked: Removes the specified data sink.
removeDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked: Removes the specified data sink.
removeDrawable(Drawable) - Method in class etomica.graphics.DisplayBox
removeDrawable(Object) - Method in class etomica.graphics.DisplayBox
removeFig(Figure) - Method in class g3dsys.control.G3DSys: Removes the Figure to from associated FigureManager
removeIntegrator(IIntegrator) - Method in class etomica.integrator.IntegratorManagerMC: Removes the given integrator from the list of integrators.
removeLine(LineSegment) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
removeListener(IBoundaryListener) - Method in interface etomica.api.IBoundaryEventManager: Removes the given listener from this event manager.
removeListener(IBoxListener) - Method in interface etomica.api.IBoxEventManager: Removes the given listener from this event manager.
removeListener(IIntegratorListener) - Method in interface etomica.api.IIntegratorEventManager: Removes the given listener from this event manager.
removeListener(ISimulationListener) - Method in interface etomica.api.ISimulationEventManager
removeListener(IBoxListener) - Method in class etomica.box.BoxEventManager
removeListener(DeviceTernarySelector.Listener) - Method in class etomica.graphics.DeviceTernarySelector
removeListener(IIntegratorListener) - Method in class etomica.integrator.IntegratorEventManager
removeListener(IIntegratorListener) - Method in class etomica.listener.IntegratorListenerGroupSeries: Removes the given action from the group.
removeListener(IListener) - Method in interface etomica.listener.ListenerGroup: Removes the given oldAction from the group.
removeListener(INeighborListListenerMolecular) - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
removeListener(INeighborListListener) - Method in class etomica.nbr.list.NeighborListEventManager
removeListener(ISimulationListener) - Method in class etomica.simulation.SimulationEventManager
removeListener(IBoundaryListener) - Method in class etomica.space.BoundaryEventManager
removeListener(IListener) - Method in class etomica.util.EventManager
removeListener(IListener) - Method in interface etomica.util.IEventManager: Removes the given listener from this event manager.
removeMCMove(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager: Removes the given MCMove from the set of moves performed by the integrator and recalculates move frequencies.
removeModel(Model) - Method in class etomica.graphics.BondListener: Informs the BondListener that bonds in molecules of the given model should no longer be tracked.
removeMolecule(IMolecule) - Method in interface etomica.api.IBox: Removes the given molecule from this box.
removeMolecule(IMolecule) - Method in class etomica.box.Box
removeMolecule(IMolecule) - Method in class etomica.nbr.cell.molecule.CellMolecular
removeMoleculeListDisplayLSMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
removeMoleculeListDisplayLSMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removeMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
removeMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removeObject(Object[], Object) - Static method in class etomica.util.Arrays: Returns an array formed by removing the given object from the given array.
removeObjectByBox(IBox) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
removeOption(String) - Method in class etomica.graphics.DeviceSelector
removeParser(ParameterParser) - Method in class etomica.util.ParameterBase
removePlane(Plane) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
removePotential(IPotentialMolecular) - Method in interface etomica.api.IPotentialMaster: Removes given potential from the group.
removePotential(IPotentialAtomic) - Method in interface etomica.api.IPotentialMaster: Removes given potential from the group.
removePotential(IPotentialMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
removePotential(IPotentialAtomic) - Method in class etomica.nbr.list.PotentialMasterList
removePotential(IPotentialMolecular) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialGroupNbr
removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialMasterHybrid
removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialMasterNbr
removePotential(IPotential) - Method in class etomica.potential.PotentialArray: Removes the given potential and the associated criterion from the list held by this type instance, and returns the index that was assigned to it.
removePotential(IPotential) - Method in class etomica.potential.PotentialArrayByType: Removes the given potential and the associated criterion from the list held by this type instance, and returns the index that was assigned to it.
removePotential(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular: Removes the given potential and the associated criterion from the list held by this type instance, and returns the index that was assigned to it.
removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup: Removes given potential from the group.
removePotential(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMaster
removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMasterMonatomic
removePotentialJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
removePotentialJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removePotParamDisplayLSMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
removePotParamDisplayLSMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removePotParamDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
removePotParamDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removePropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
removePropertyChangeListener(PropertyChangeListener) - Method in class etomica.util.Grabber.ActionCornerSetter
removeRange(int, int) - Method in class etomica.util.ObjectArrayList: Removes from this List all of the elements whose index is between fromIndex, inclusive and toIndex, exclusive.
removeSpecies(ISpecies) - Method in interface etomica.api.ISimulation: Removes the given ISpecies from the ISimulation.
removeSpecies(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
removeSpecies(ISpecies) - Method in class etomica.simulation.Simulation
removeSpecies() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
removeSpeciesAtIndex(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
removeSpeciesJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
removeSpeciesJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
removeSpeciesMolecule(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
removeSpeciesNotify(ISpecies) - Method in interface etomica.api.IBox: Notifies the IBox that a Species has been removed.
removeSpeciesNotify(ISpecies) - Method in class etomica.box.Box
removeValueChangedListener(DeviceBoxValueChangedListener) - Method in class etomica.graphics.DeviceBox: Remove an object that is listening for the DeviceBox value to change
renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
renderAllStrings(Object) - Method in class org.jmol.util.GData
renderBackground(Graphics3D) - Method in class org.jmol.g3d.Graphics3D
renderBackground(Graphics3D) - Method in class org.jmol.util.GData
renderCrossHairs(int[], int, int, Point3f, float) - Method in class org.jmol.g3d.Graphics3D
renderHermiteRibbon(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, int) - Method in class org.jmol.g3d.HermiteRenderer
renderHermiteRope(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.HermiteRenderer
RenderMD - Class in etomica.modules.render: Three-dimensional hard-sphere molecular dynamics simulation, using neighbor listing.
RenderMD(ISpace) - Constructor for class etomica.modules.render.RenderMD: Sole public constructor, makes a simulation using a 3D space.
RenderMD(ISpace, RenderMD.RenderMDParam) - Constructor for class etomica.modules.render.RenderMD
RenderMD.CriterionCar - Class in etomica.modules.render
RenderMD.P2PenetrableCar - Class in etomica.modules.render
RenderMD.RenderMDParam - Class in etomica.modules.render: Inner class for parameters understood by the HSMD3D constructor
RenderMDGraphic - Class in etomica.modules.render
RenderMDGraphic(RenderMD, Space) - Constructor for class etomica.modules.render.RenderMDGraphic
RenderMDParam() - Constructor for class etomica.modules.render.RenderMD.RenderMDParam
repaint() - Method in class etomica.graphics.Display
repaint() - Method in class etomica.graphics.DisplayBox: Repaint the graphic associated with the display box.
repaint() - Method in class etomica.graphics.DisplayCanvas
repaint() - Method in class etomica.graphics.DisplayPolytope
repaint() - Method in class etomica.graphics.DisplayTable
repaint() - Method in class etomica.graphics.PropertyText
repaint(Object) - Method in interface org.jmol.api.ApiPlatform
repaint(Object) - Method in class org.jmol.awt.Platform
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
repaintSleep - Variable in class etomica.graphics.SimulationGraphic
repaintwaitms - Static variable in class org.jmol.script.Token
replaceAllCharacter(String, String, char) - Static method in class org.jmol.util.TextFormat: Does a clean replace of any of the characters in str with chrTo If strTo contains strFrom, then only a single pass is done.
replaceAllCharacters(String, String, String) - Static method in class org.jmol.util.TextFormat: Does a clean replace of any of the characters in str with strTo If strTo contains strFrom, then only a single pass is done.
replaceQuotedStrings(Vector, Vector, String, int) - Static method in class etomica.util.ScientificFormat
replaceQuotedStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
replaceStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
replicate(Configuration, IBox, int[], ISpace) - Static method in class etomica.config.ConfigurationFileBinary: Reads the configuration from the file and then replicates the configuration reps times in each direction.
replicate(Configuration, IBox, int[], ISpace) - Static method in class etomica.config.ConfigurationReplicate: Replicates the configuration from config within boxBig.
REPULSION_ATTRACTION - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
REPULSION_ONLY - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
requestFocusInWindow(Object) - Method in interface org.jmol.api.ApiPlatform
requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
Requirement - Class in etomica.compatibility
Requirement() - Constructor for class etomica.compatibility.Requirement
RequirementSet - Class in etomica.compatibility
rescale(Configuration, IBox, double, ISpace) - Static method in class etomica.config.ConfigurationFileBinary
rescaleBox(double) - Method in class etomica.normalmode.SimFluidSoftSphere
rescalingToFitVolume - Variable in class etomica.config.ConfigurationLattice
rescalingToFitVolume - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
rescalingToFitVolume - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
reservoir - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
reservoirCount - Variable in class etomica.box.Box
reservoirSize - Variable in class etomica.atom.AtomLeafAgentManager
reservoirSize - Variable in class etomica.atom.MoleculeAgentManager
reservoirSize - Variable in class etomica.box.Box
reset() - Method in class etomica.action.activity.ActivityGroupSeries: Marks all actions as pending.
reset() - Method in class etomica.action.activity.Controller
RESET - Static variable in class etomica.action.activity.ControllerEvent
reset() - Method in interface etomica.action.activity.IController: Marks all actions as pending.
reset() - Method in interface etomica.api.IIntegrator: Defines the actions taken by the integrator to reset itself, such as required if a perturbation is applied to the simulated box (e.g., addition or deletion of a molecule).
reset() - Method in class etomica.atom.AtomLeafAgentManager.AgentIterator
reset() - Method in class etomica.atom.AtomTypeAgentManager.AgentIterator
reset() - Method in class etomica.atom.iterator.ANIntergroupCoupled
reset() - Method in class etomica.atom.iterator.ANIntergroupExchange
reset() - Method in class etomica.atom.iterator.ANIntragroupExchange
reset() - Method in class etomica.atom.iterator.ApiIndexList: Resets iterator to a state where hasNext is true, if atoms in pair are not null.
reset() - Method in class etomica.atom.iterator.ApiInnerVariable: Resets the iterator, so that it is ready to go through all of its pairs.
reset() - Method in class etomica.atom.iterator.ApiInterArrayList: Sets iterator in condition to begin iteration.
reset() - Method in class etomica.atom.iterator.ApiIntergroup
reset() - Method in class etomica.atom.iterator.ApiIntergroupCoupled
reset() - Method in class etomica.atom.iterator.ApiIntergroupExchange
reset() - Method in class etomica.atom.iterator.ApiIntraArrayList: Sets iterator in condition to begin iteration.
reset() - Method in class etomica.atom.iterator.ApiIntragroup: Puts iterator in a state to begin iteration.
reset() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
reset() - Method in class etomica.atom.iterator.AtomIteratorArrayList: Puts iterator in state ready to begin iteration.
reset() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Readies the iterator to begin iteration.
reset() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Puts iterator in state ready to begin iteration.
reset() - Method in class etomica.atom.iterator.AtomIteratorBasis: Puts iterator in a state ready to begin iteration.
reset() - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart: Puts iterator in a state ready to begin iteration.
reset() - Method in class etomica.atom.iterator.AtomIteratorNull
reset() - Method in class etomica.atom.iterator.AtomIteratorSinglet: Resets iterator to a state where hasNext is true.
reset() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList: Resets iterator to a state where hasNext is true, if atoms in pair are not null.
reset() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList: Resets iterator to a state where hasNext is true, if atoms in pair are not null.
reset() - Method in interface etomica.atom.iterator.AtomsetIterator: Resets the iterator to loop through its iterates again.
reset() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
reset() - Method in class etomica.atom.iterator.MoleculeIteratorAll
reset() - Method in class etomica.atom.iterator.MoleculeIteratorArrayList: Puts iterator in state ready to begin iteration.
reset() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Puts iterator in state ready to begin iteration.
reset() - Method in class etomica.atom.iterator.MoleculeIteratorMolecule
reset() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet: Resets iterator to a state where hasNext is true.
reset() - Method in class etomica.atom.iterator.MpiInnerFixed: Resets the iterator, so that it is ready to go through all of its pairs.
reset() - Method in class etomica.atom.iterator.MpiInnerVariable: Resets the iterator, so that it is ready to go through all of its pairs.
reset() - Method in class etomica.atom.iterator.MpiInterArrayList: Sets iterator in condition to begin iteration.
reset() - Method in class etomica.atom.iterator.MpiInterspecies1A
reset() - Method in class etomica.atom.iterator.MpiInterspeciesAA: Sets iterator in condition to begin iteration.
reset() - Method in class etomica.atom.iterator.MpiIntraArrayList: Sets iterator in condition to begin iteration.
reset() - Method in class etomica.atom.iterator.MpiIntraspecies1A
reset() - Method in class etomica.atom.iterator.MpiIntraspeciesAA: Sets iterator in condition to begin iteration.
reset() - Method in class etomica.atom.iterator.MpiMolecule: Readies iterator for iteration.
reset() - Method in class etomica.atom.iterator.TripletInnerSequential
reset() - Method in class etomica.atom.MoleculeAgentManager.AgentIterator
reset() - Method in class etomica.atom.SpeciesAgentManager.AgentIterator
reset() - Method in class etomica.box.BoxAgentManager.AgentIterator
reset() - Method in class etomica.config.ConformationChain: Resets the vector instructions.
reset() - Method in class etomica.config.ConformationChain2D
reset() - Method in class etomica.config.ConformationChain3D
reset() - Method in class etomica.config.ConformationChainZigZag
reset() - Method in class etomica.config.ConformationChainZigZag2
reset() - Method in class etomica.data.AccumulatorAverage: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageBlockless: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageBlocklessSlim: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageCollapsing: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageCollapsingLog: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageCovariance
reset() - Method in class etomica.data.AccumulatorAverageFixed: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorAverageFixedOutputFile: Resets all sums to zero.
reset() - Method in class etomica.data.AccumulatorCounter: Sets count to zero.
reset() - Method in class etomica.data.AccumulatorHistogram: Zeros histograms, discarding any previous contributions.
reset() - Method in class etomica.data.AccumulatorHistory
reset() - Method in class etomica.data.AccumulatorRatioAverage
reset() - Method in class etomica.data.AccumulatorRatioAverageCovariance
reset() - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
reset() - Method in class etomica.data.DataAccumulator: Defined by subclass to perform some action that clears accumulated values.
reset() - Method in class etomica.data.DataArrayWriter
reset() - Method in interface etomica.data.DataLogger.DataWriter: Informs the DataSink that it will be writing the beginning of the file so printing header information is appropriate.
reset() - Method in class etomica.data.DataPumpListenerPow
reset() - Method in class etomica.data.DataPumpListenerPowStrict
reset() - Method in class etomica.data.DataSet
reset() - Method in class etomica.data.DataTableWriter
reset() - Method in class etomica.data.meter.MeterDihedralAngle: Zero's out the G(phi) sum tracked by this meter.
reset() - Method in class etomica.data.meter.MeterMeanSquareDisplacement: Specifies the set of atoms that will be tracked to compute their MSD.
reset() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
reset() - Method in class etomica.data.meter.MeterPressureHard
reset() - Method in class etomica.data.meter.MeterProfile
reset() - Method in class etomica.data.meter.MeterProfileByAtoms
reset() - Method in class etomica.data.meter.MeterProfileByVolume
reset() - Method in class etomica.data.meter.MeterRDF: Zero's out the RDF sum tracked by this meter.
reset() - Method in class etomica.data.meter.MeterRDFPC: Zero's out the RDF sum tracked by this meter.
reset() - Method in class etomica.data.meter.MeterStructureFactor
reset() - Method in class etomica.data.meter.PotentialCalculationRDF: Zero's out the RDF sum tracked by this meter.
reset() - Method in class etomica.dimer.IntegratorDimerMin
reset() - Method in class etomica.dimer.IntegratorDimerRT
reset() - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB: Zeros out the pressureTensor.
reset() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
reset() - Method in class etomica.graphics.DeviceControllerButton: Sets label of button to display "Start".
reset() - Method in class etomica.graphics.DeviceTrioControllerButton: Sets controller toggle button to read "Start"
reset() - Method in class etomica.integrator.Integrator: Defines the actions taken by the integrator to reset itself, such as required if a perturbation is applied to the simulated box (e.g., addition or deletion of a molecule).
reset() - Method in class etomica.integrator.IntegratorBox: Defines the actions taken by the integrator to reset itself, such as required if a perturbation is applied to the simulated box (e.g., addition or deletion of a molecule).
reset() - Method in class etomica.integrator.IntegratorGear4
reset() - Method in class etomica.integrator.IntegratorGear4NPH
reset() - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp: resets the "atom" held by this class, ensuring the method will work even if (coincidentally) the atom is the same as the same one as the last time the method was called.
reset() - Method in class etomica.integrator.IntegratorHard
reset() - Method in class etomica.integrator.IntegratorManagerMC: Causes recalculation of move frequencies and zero of selection counts for moves.
reset() - Method in class etomica.integrator.IntegratorMC: Causes recalculation of move frequencies and zero of selection counts for moves.
reset() - Method in class etomica.integrator.IntegratorMD: reset the integrator's kinetic energy tracker
RESET - Static variable in class etomica.integrator.IntegratorNonintervalEvent
reset() - Method in class etomica.integrator.IntegratorRigidIterative
reset() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
reset() - Method in class etomica.integrator.IntegratorVelocityVerlet
reset() - Method in class etomica.integrator.IntegratorVelocityVerletRattle
reset() - Method in class etomica.integrator.IntegratorVelocityVerletShake
reset() - Method in class etomica.integrator.IntegratorVerlet
reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
reset() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
reset() - Method in class etomica.integrator.mcmove.MCMoveTracker
reset() - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce: Re-zeros the force vector.
reset() - Method in class etomica.lattice.CellLattice.NeighborIterator
reset() - Method in interface etomica.lattice.IndexIterator
reset() - Method in class etomica.lattice.IndexIteratorIncreasing: Resets the iterator.
reset() - Method in class etomica.lattice.IndexIteratorRectangular: Puts iterator in a condition to begin iteration.
reset() - Method in class etomica.lattice.IndexIteratorReflecting
reset() - Method in class etomica.lattice.IndexIteratorTriangular: Sets iterator to begin returning iterates.
reset() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
reset() - Method in class etomica.lattice.RectangularLattice.Iterator
reset() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Resets the iterator to loop through its iterates again.
reset() - Method in interface etomica.lattice.SiteIterator: Puts the iterator in a state ready to begin iteration.
reset() - Method in class etomica.mappedvirial.MappedUpotential
reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
reset() - Method in class etomica.math.discrete.CombinationIterator
reset() - Method in class etomica.math.discrete.FixedSumIterator: Sets the iterator to begin iteration.
reset() - Method in class etomica.math.discrete.PermutationDegenerateIterator: Readies the iterator for iteration.
reset() - Method in class etomica.math.discrete.PermutationIterator
reset() - Method in class etomica.metastable.MeterDensityDistribution
reset() - Method in class etomica.models.nitrogen.MeterNormalizedCoord: Sets the tensor summation to 0.
reset() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta: Sets the tensor summation to 0.
reset() - Method in class etomica.models.nitrogen.MeterOrientationDistribution: Sets the tensor summation to 0.
reset() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup: Sets the tensor summation to 0.
reset() - Method in class etomica.modules.adsorption.EOSSW
reset() - Method in class etomica.modules.adsorption.EOSSWPatel
reset() - Method in class etomica.modules.adsorption.IntegratorHybrid
reset() - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
reset() - Method in class etomica.modules.adsorption.ModifierPMu
reset() - Method in class etomica.modules.adsorption.VEOS3SW
reset() - Method in class etomica.modules.catalysis.InteractionTracker
reset() - Method in class etomica.modules.chainequilibrium.MeterChainLength
reset(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
reset() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
reset() - Method in class etomica.modules.droplet.IntegratorDroplet
reset() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
reset() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
reset() - Method in class etomica.modules.joulethomson.IntegratorJT
reset() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
reset() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
reset() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2: Resets all sums to zero
reset() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
reset() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
reset() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
reset(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
reset() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce: Re-zeros the force vectors.
reset() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce: Re-zeros the force vectors.
reset(IAtom) - Method in class etomica.modules.sam.CriterionTether3
reset() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
reset() - Method in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
reset() - Method in class etomica.nbr.cell.Api1ACell
reset() - Method in class etomica.nbr.cell.ApiAACell
reset() - Method in class etomica.nbr.cell.AtomIteratorCell
reset() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
reset() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
reset() - Method in class etomica.nbr.cell.molecule.MpiAACell
reset() - Method in class etomica.nbr.cell.PotentialMasterCell: Reassign atoms to cell lists for all boxes.
reset(IAtom) - Method in class etomica.nbr.CriterionAdapter: Indicates to wrapped criterion that given atom's neighbor list has just been updated, and that properties (e.g., record of atom's position) used by needUpdate and unsafe() methods should be reset.
reset(IAtom) - Method in class etomica.nbr.CriterionAll: Performs no action.
reset(IAtom) - Method in class etomica.nbr.CriterionNone: Performs no action.
reset(IAtom) - Method in class etomica.nbr.CriterionPositionWall
reset(IAtom) - Method in class etomica.nbr.CriterionSimple
reset() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: For each box in the array, applies central image, resets neighbors of all atoms, and sets up all neighbor lists.
reset() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Recomputes the maximum potential range (which might change without this class receiving notification) and readjust cell lists
reset() - Method in class etomica.nbr.list.NeighborListManager: For each box in the array, applies central image, resets neighbors of all atoms, and sets up all neighbor lists.
reset() - Method in class etomica.nbr.list.PotentialMasterList: Recomputes the maximum potential range (which might change without this class receiving notification) and readjust cell lists
reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular: Indicates to wrapped criterion that given atom's neighbor list has just been updated, and that properties (e.g., record of atom's position) used by needUpdate and unsafe() methods should be reset.
reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionAllMolecular: Performs no action.
reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
reset(IMolecule) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular: Indicates to criterion that given molecule's neighbor list has just been updated, and that properties (e.g., record of molecule's position) used by needUpdate and unsafe() methods should be reset.
reset(IAtom) - Method in interface etomica.nbr.NeighborCriterion: Indicates to criterion that given atom's neighbor list has just been updated, and that properties (e.g., record of atom's position) used by needUpdate and unsafe() methods should be reset.
reset() - Method in class etomica.nbr.site.Api1ASite
reset() - Method in class etomica.normalmode.HSNPT.ActionSummer
reset() - Method in class etomica.normalmode.IntegratorHardMDMC
reset() - Method in class etomica.normalmode.MeterNormalMode: Sets the tensor summation to 0.
reset() - Method in class etomica.normalmode.MeterTiltHistogram
reset() - Method in class etomica.normalmode.MeterTiltRotationHistogram
reset() - Method in class etomica.normalmode.PotentialCalculationEFSSP: Sets the virial sum to zero, typically to begin a new virial-sum calculation.
reset() - Method in class etomica.normalmode.PotentialCalculationLJSP: Sets the virial sum to zero, typically to begin a new virial-sum calculation.
reset() - Method in class etomica.overlap.IntegratorOverlap
reset() - Method in class etomica.potential.PotentialCalculationForcePressureSum: Zeros out the pressureTensor.
reset() - Method in class etomica.potential.PotentialCalculationForceSum: Re-zeros the force vectors.
reset() - Method in class etomica.potential.PotentialCalculationTorqueSum: Re-zeros the force vectors.
reset() - Method in class etomica.potential.PotentialMaster.AtomIterator0
reset() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
reset() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
reset() - Method in interface etomica.space.RotationTensor: Sets tensor to a condition of no rotation.
reset() - Method in class etomica.space2d.RotationTensor2D
reset() - Method in class etomica.space3d.RotationTensor3D
reset() - Method in class etomica.thermointegration.IntegratorThermodynamic: Resets this integrator and passes on the reset to the subIntegrator.
reset() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
reset() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
reset() - Method in interface etomica.util.Histogram: resets all histogram values and counts to zero
reset() - Method in class etomica.util.HistogramCollapsing
reset() - Method in class etomica.util.HistogramDiscrete
reset() - Method in class etomica.util.HistogramExpanding
reset() - Method in class etomica.util.HistogramNotSoSimple
reset() - Method in class etomica.util.HistogramReweightedData
reset() - Method in class etomica.util.HistogramSimple
reset() - Method in interface etomica.util.History: Resets the History.
reset() - Method in class etomica.util.HistoryCollapsing: Removes entire history, setting all values to NaN.
reset() - Method in class etomica.util.HistoryCollapsingAverage
reset() - Method in class etomica.util.HistoryComplete: Removes entire history, setting all values to NaN.
reset() - Method in class etomica.util.HistoryScrolling: Removes entire history, setting all values to NaN.
reset() - Method in class etomica.util.TreeList: clear the tree by disconnecting everything from the head.
reset() - Method in class etomica.virial.cluster.ClusterDiagram: Resets the cluster to being fully connected except that root points are not connected to each other.
reset() - Method in class etomica.virial.cluster.ClusterGenerator: Resets the cluster generator.
reset() - Method in class etomica.virial.cluster.PermutationIterator
reset(long) - Method in class etomica.virial.CoordinatePairLeafSet
reset(long) - Method in class etomica.virial.CoordinatePairMoleculeSet
reset(long) - Method in interface etomica.virial.CoordinatePairSet: Informs the CoordinatePairSet that the configuration has changed and that it has a new ID
reset() - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
reset() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies: Reset to initial value.
reset() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
reset() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
reset() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
reset() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
reset() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
reset() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: Resets all sums to zero
reset() - Method in class etomica.virial.overlap.DataSourceVirialOverlap: Convenience method that resets reference and target accumulators
reset() - Method in class etomica.virial.overlap.DataVirialOverlap: Convenience method that resets reference and target accumulators
reset() - Method in class etomica.virial.overlap.IntegratorOverlap
reset() - Method in interface g3dsys.control.IndexIterator: Resets iteration; should be called before use
reset() - Method in class org.jmol.util.BoxInfo
ResetAccumulators - Class in etomica.action
ResetAccumulators() - Constructor for class etomica.action.ResetAccumulators
ResetAccumulatorsAveraged - Class in etomica.action
ResetAccumulatorsAveraged() - Constructor for class etomica.action.ResetAccumulatorsAveraged
resetAction - Variable in class etomica.graphics.DeviceNSelector
resetAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
resetAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
resetAdjustStep() - Method in class etomica.integrator.mcmove.MCMoveStepTracker: Resets damped step adjustment.
resetAxes() - Method in class etomica.graphics.EtomicaPlot: Overrides a not-so-useful method in superclass
resetBonds() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
resetBonds() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
resetCollision() - Method in class etomica.integrator.IntegratorHard.Agent: resets collision potential and partner.
resetCollisionFull() - Method in class etomica.integrator.IntegratorHard.Agent: resets time, potential and partner.
resetCollisionTimes() - Method in class etomica.integrator.IntegratorHard: Do an upList call for each atom and reconstruct the event list.
resetFilter() - Method in interface etomica.atom.AtomFilterCollective: Informs the filter that something in the system has changed (atom positions, velocityies, etc) has changed and the filtered status of the atoms should be determined.
resetFilter() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquid
resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
resetNewMoleculePair() - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
resetNewMoleculePair() - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
resetPiston() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
resetRotation() - Method in class etomica.config.GrainBoundaryTiltConfiguration
resetScale() - Method in class etomica.graphics.DisplayScrollingGraph
resetSelectionViewANew() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
resetSlab() - Method in class org.jmol.util.MeshSurface
resetStepCount() - Method in interface etomica.api.IIntegrator: This method resets the step counter.
resetStepCount() - Method in class etomica.integrator.Integrator
resetStepCount() - Method in class etomica.integrator.IntegratorMD
resetStepCount() - Method in class etomica.modules.adsorption.IntegratorHybrid
resetViewAfterSSSPException() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
resetViewToDisplaySpecies1() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
reshape(int, int) - Method in class etomica.graphics.DisplayCanvas: Same as setSize, but included to implement DisplayCanvasInterface, which has this for compatibility with OpenGL.
residual - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
residue - Static variable in class org.jmol.script.Token
resizeArray(Object[], int) - Static method in class etomica.util.Arrays: Returns a new array holding the objects in the given array, but adjusted to the given size.
resizeArray(double[], int) - Static method in class etomica.util.Arrays: Returns a new array holding the values in the given array, but adjusted to the given size.
resizeArray(int[], int) - Static method in class etomica.util.Arrays: Returns a new array holding the values in the given array, but adjusted to the given size.
resizeArray(long[], int) - Static method in class etomica.util.Arrays
resizeArray(boolean[], int) - Static method in class etomica.util.Arrays: Returns a new array holding the values in the given array, but adjusted to the given size.
resizeData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
resizeData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
resizeDimer() - Method in class etomica.dimer.IntegratorDimerRT
resizeGraphic() - Method in class etomica.graphics.DevicePlotPoints: Returns the top level panel that the plot scale resizing components sit on.
resno - Static variable in class org.jmol.script.Token
RESOURCES - Static variable in class etomica.graph.view.rasterizer.Messages: The error messages bundle class name.
restartAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
resume - Static variable in class org.jmol.script.Token
retainAll(Collection<?>) - Method in class etomica.graph.model.GraphList
returnMu - Variable in class etomica.normalmode.DataSourcePMu
ReturnValue(int, ISpace) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
reverse(double[], double) - Static method in class etomica.util.SineTransform
reverse - Static variable in class org.jmol.script.Token
reverseCollisionHandler - Variable in class etomica.integrator.IntegratorHard
ReverseOsmosis - Class in etomica.modules.rosmosis: Reverse osmosis simulation, based on simulation code by Sohail Murad.
ReverseOsmosis(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosis
ReverseOsmosisGraphic - Class in etomica.modules.rosmosis: Graphical and data collection bits for reverse osmosis simulation.
ReverseOsmosisGraphic(ReverseOsmosis, Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic
ReverseOsmosisGraphic.Applet - Class in etomica.modules.rosmosis
ReverseOsmosisGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
ReverseOsmosisGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
ReverseOsmosisGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
ReverseOsmosisWater - Class in etomica.modules.rosmosis: Reverse osmosis simulation, based on simulation code by Sohail Murad.
ReverseOsmosisWater(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWater
ReverseOsmosisWaterGraphic - Class in etomica.modules.rosmosis: Graphical and data collection bits for reverse osmosis simulation.
ReverseOsmosisWaterGraphic(ReverseOsmosisWater) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
ReverseOsmosisWaterGraphic.Applet - Class in etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
ReverseOsmosisWaterGraphic.ModifierSoluteCharge - Class in etomica.modules.rosmosis
revertDiagram() - Method in class etomica.virial.ClusterSumStickyEF: set the diagram used for calculating the value to the ith diagram.
revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
revertF() - Method in class etomica.virial.ClusterTree
rewind - Static variable in class org.jmol.script.Token
rFill(StringXBuilder, String, String) - Static method in class org.jmol.util.TextFormat
rfit - Static variable in class etomica.potential.P2O2Bartolomei
rfit0 - Static variable in class etomica.potential.P2O2Bartolomei
rfitMRCI - Static variable in class etomica.potential.P2O2Bartolomei
rfitPT2 - Static variable in class etomica.potential.P2O2Bartolomei
rg - Variable in class etomica.modules.droplet.MeterDeformation
rgb(int, int, int) - Static method in class org.jmol.util.ColorUtil
Rgb16 - Class in org.jmol.util
Rgb16() - Constructor for class org.jmol.util.Rgb16
RheologyGraphic - Class in etomica.modules.rheology: Module for "Macromolecular dynamics related to rheological properties through Brownian dynamics simulations", designed by Lewis Wedgewood.
RheologyGraphic(SimulationRheology) - Constructor for class etomica.modules.rheology.RheologyGraphic
RheologyGraphic.Applet - Class in etomica.modules.rheology
rho - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
rho - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
rho - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
rho - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
rho - Variable in class etomica.util.numerical.B9Optimizer
rho - Variable in class etomica.util.numerical.VirialOptimizer
rho - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
rho - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
rho - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
rho - Variable in class etomica.virial.cluster.VirialDiagrams
rho - Variable in class etomica.virial.cluster.VirialDiagramsPT
rho - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
rho - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rho0 - Variable in class etomica.meam.ParameterSetMEAM
rho0 - Static variable in class etomica.statmech.HardSphereSolid
rho0 - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
rho0 - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
rho0point - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
rho1 - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoA - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
rhoA - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoA - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
rhoA - Variable in class etomica.virial.cluster.VirialDiagramsMix
rhoA - Variable in class etomica.virial.cluster.VirialDiagramsMix2
rhoA - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
rhoA - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoAB - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
rhoAB - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoAB - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
rhoAB - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
rhoAB - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoAB0 - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
rhoABC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoABC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoAC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoAC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoAlphaTrans - Variable in class etomica.models.nitrogen.FindTransitionTemperature
rhoB - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
rhoB - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoB - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
rhoB - Variable in class etomica.virial.cluster.VirialDiagramsMix
rhoB - Variable in class etomica.virial.cluster.VirialDiagramsMix2
rhoB - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
rhoB - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoBC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoBC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoBetaTrans - Variable in class etomica.models.nitrogen.FindTransitionTemperature
rhoC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
rhoc - Static variable in class etomica.modules.adsorption.EOSSW
rhoC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
rhoForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
rhograd - Variable in class etomica.meam.PotentialCuLREP
rhograd - Variable in class etomica.meam.PotentialEFS
rhograd - Variable in class etomica.meam.PotentialFeEAM
rhograd - Variable in class etomica.meam.PotentialFeEAM_LS
rhoi(IAtomList) - Method in class etomica.meam.PotentialMEAM
rhoi1sq() - Method in class etomica.meam.PotentialMEAM
rhoi2sq() - Method in class etomica.meam.PotentialMEAM
rhoi3sq() - Method in class etomica.meam.PotentialMEAM
RHOj0 - Static variable in class etomica.meam.PotentialMEAM
RHOj1x - Static variable in class etomica.meam.PotentialMEAM
RHOj1y - Static variable in class etomica.meam.PotentialMEAM
RHOj1z - Static variable in class etomica.meam.PotentialMEAM
RHOj2 - Static variable in class etomica.meam.PotentialMEAM
RHOj2xx - Static variable in class etomica.meam.PotentialMEAM
RHOj2xy - Static variable in class etomica.meam.PotentialMEAM
RHOj2xz - Static variable in class etomica.meam.PotentialMEAM
RHOj2yy - Static variable in class etomica.meam.PotentialMEAM
RHOj2yz - Static variable in class etomica.meam.PotentialMEAM
RHOj2zz - Static variable in class etomica.meam.PotentialMEAM
RHOj3xxx - Static variable in class etomica.meam.PotentialMEAM
RHOj3xxy - Static variable in class etomica.meam.PotentialMEAM
RHOj3xxz - Static variable in class etomica.meam.PotentialMEAM
RHOj3xyy - Static variable in class etomica.meam.PotentialMEAM
RHOj3xyz - Static variable in class etomica.meam.PotentialMEAM
RHOj3xzz - Static variable in class etomica.meam.PotentialMEAM
RHOj3yyy - Static variable in class etomica.meam.PotentialMEAM
RHOj3yyz - Static variable in class etomica.meam.PotentialMEAM
RHOj3yzz - Static variable in class etomica.meam.PotentialMEAM
RHOj3zzz - Static variable in class etomica.meam.PotentialMEAM
rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
rhopoint - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
rHSCore - Static variable in class etomica.potential.P2WaterPotentialsJankowski
ri - Variable in class etomica.models.co2.P2CO2Hellmann
ri - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
ri - Variable in class etomica.potential.P3Induction
ribbon - Static variable in class org.jmol.script.Token
ribbonaspectratio - Static variable in class org.jmol.script.Token
ribbonborder - Static variable in class org.jmol.script.Token
RIGHT - Static variable in class etomica.graphics.DisplayBox
RIGHT - Static variable in class etomica.graphics.DisplayPolytope
RIGHT - Static variable in class etomica.util.Constants.Direction
right - Static variable in class org.jmol.script.Token
rightAngle - Static variable in class etomica.lattice.crystal.Primitive
rightDifference(Quaternion) - Method in class org.jmol.util.Quaternion
rij - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
rij - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
rij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
Rij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
rij - Variable in class etomica.normalmode.PotentialCalculationLJSP
Rij - Variable in class etomica.normalmode.PotentialCalculationLJSP
rij - Variable in class etomica.potential.P3Induction
rijVector - Variable in class etomica.models.co2.PNCO2GCPM
rijVector - Variable in class etomica.models.co2.PNGCPM
rijVector - Variable in class etomica.models.water.PNWaterGCPM
rik - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
rik - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
rik - Variable in class etomica.potential.P3Induction
rIndices - Variable in class etomica.virial.cluster.PermutationIterator
Ring - Class in etomica.virial.cluster
Ring(int) - Constructor for class etomica.virial.cluster.Ring: Constructor for Ring.
ring(int) - Static method in class etomica.virial.cluster.Standard: Returns a ring of bonds, {{0,1},{1,2},...{n-2,n-1},{n-1,0}}
ring0 - Variable in class etomica.virial.simulations.ModifierTPI
ring1 - Variable in class etomica.virial.simulations.ModifierTPI
RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
RING_TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
RING_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
RING_TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
ringFrac - Variable in class etomica.virial.ClusterChainHS
ringFrac - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
ringFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
ringFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
ringFrac - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
ringFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
ringFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
ringFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
ringHS(int) - Static method in class etomica.virial.cluster.Standard: Return integral for ring of hard spheres of size nPoints
ringResult - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
RingResult() - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
rings - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
RINGS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
RINGS - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
RINGS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
rj - Variable in class etomica.models.co2.P2CO2Hellmann
rj - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
rj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
rj - Variable in class etomica.potential.P3Induction
rjk - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
rjk - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
rjrj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
rk - Variable in class etomica.potential.P3Induction
rkl - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
rLast - Variable in class etomica.data.meter.MeterMeanSquareDisplacement
rm() - Method in interface etomica.api.IAtomType: Returns the reciprocal of the mass, 1.0/mass
rm() - Method in interface etomica.api.IElement
rm() - Method in class etomica.atom.AtomTypeLeaf
rm() - Method in class etomica.chem.elements.Element
rm - Variable in class etomica.chem.elements.ElementChemical
rm() - Method in class etomica.chem.elements.ElementChemical
rm - Variable in class etomica.chem.elements.ElementSimple
rm() - Method in class etomica.chem.elements.ElementSimple
rMax - Variable in class etomica.data.meter.MeterDihedralAngle
rMax - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
rmax - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
rMaxSafe - Variable in class etomica.nbr.CriterionPositionWall
rMin - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
rMin - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
rMin - Static variable in class etomica.potential.P2HydrogenPatkowski
rMin - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
rMin - Static variable in class etomica.potential.P2O2Bartolomei
rMrLast - Variable in class etomica.integrator.IntegratorVerlet.Agent
rna - Static variable in class org.jmol.script.Token
rocket - Static variable in class org.jmol.script.Token
rocketbarrels - Static variable in class org.jmol.script.Token
rOM - Static variable in class etomica.models.water.ConformationWaterTIP4P
root(int, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The integer root.
root(int) - Method in class etomica.veos.bigdecimal.Ifactor: Pulling the r-th root.
root(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: r-th root.
rootD(double) - Method in interface etomica.space.ISpace: Returns the given value raised to the power 1/D, where D is the dimension of the space.
rootD(double) - Method in class etomica.space.Space
rootD(double) - Method in class etomica.space1d.Space1D: Returns the Dth root of the given value, a^(1/D), where D is the dimension of the space.
rootD(double) - Method in class etomica.space2d.Space2D: Returns the square root of the given value, a^(1/D), which is a^(1/2).
rootD(double) - Method in class etomica.space3d.Space3D: Returns the cube root of the given value, a^(1/D) which is a^(1/3).
rootDeg(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Compute the order of the root r.
rootPointsSpecial - Static variable in class etomica.graph.model.impl.MetadataImpl
rot - Variable in class etomica.models.hexane.TestHexane
rot - Variable in class etomica.models.hexane.TestHexaneFileConfig
rot - Variable in class etomica.models.hexane.TestHexaneHarmonic
rot - Variable in class etomica.models.hexane.TestSetToUHexane
rot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
rot0 - Variable in class etomica.models.co2.P2CO2H2OWheatley
rot0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
rot0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
rot1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
rot1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
rot1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
rotate - Variable in class etomica.dimer.IntegratorDimerMin
rotate - Variable in class etomica.dimer.IntegratorDimerRT
rotate - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
rotate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
rotate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
rotate - Static variable in class org.jmol.script.Token
rotate(Matrix4f) - Method in class org.jmol.util.Quadric
rotateBy(double, double, IVector, IVectorMutable) - Static method in class etomica.potential.P2NitrogenHellmann
rotateBy(double) - Method in interface etomica.space2d.IOrientation2D: Rotate the orientation by the amount dt (radians) in the counter-clockwise direction.
rotateBy(double) - Method in class etomica.space2d.Orientation2D: Rotates orientation around the given axis by the given value.
rotateBy(double, IVector) - Method in interface etomica.space3d.IOrientation3D: Rotate the orientation by the amount dt (radians) about the given axis.
rotateBy(double, IVector) - Method in class etomica.space3d.Orientation3D: Rotates orientation by the given value about the given axis.
rotateBy(double, IVector) - Method in class etomica.space3d.OrientationFull3D: Rotates orientation by the given value about the given axis.
rotateByX(float) - Method in class g3dsys.control.G3DSys: Rotate the display around the x axis
rotateByXY(float, float) - Method in class g3dsys.control.G3DSys: Rotate the display around the x and y axes
rotateByY(float) - Method in class g3dsys.control.G3DSys: Rotate the display around the y axis
rotateByZ(float) - Method in class g3dsys.control.G3DSys: Rotate the display around the z axis
rotateDimerNewton() - Method in class etomica.dimer.IntegratorDimerMin: Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest curvature mode.
rotateDimerNewton() - Method in class etomica.dimer.IntegratorDimerRT: Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest curvature mode.
rotateMolecule - Variable in class etomica.AlkaneEH.CH4NVT
rotateMolecule - Variable in class etomica.AlkaneEH.DHS_NVT
rotateMolecule - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
rotateMolecule - Variable in class etomica.dielectric.DHS_NVT
rotateMolecule - Variable in class etomica.dielectric.DLJ_NVT_1site
rotateMolecule - Variable in class etomica.dielectric.TIP4P_NVT
rotateOrientation(OrientationFull3D) - Method in class etomica.math.Quaternion: Rotates the input orientation by using the Quaternion rotation operator L(v) = qvq*.
rotatePhi - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
rotateTensor - Variable in class etomica.virial.MCMoveClusterRotateCH3
rotateTensor - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
rotateToHome() - Method in class g3dsys.control.G3DSys: Remove all rotation (and translation) and return to the home position
rotateToX(float) - Method in class g3dsys.control.TransformManager
rotateToY(float) - Method in class g3dsys.control.TransformManager
rotateToZ(float) - Method in class g3dsys.control.TransformManager
rotateVector(IVectorMutable) - Method in class etomica.math.Quaternion: Rotates the input vector by using the Quaternion rotation operator L(v) = qvq*.
rotation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
rotation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
rotation - Variable in class etomica.models.nitrogen.TestRotationVector
rotation - Static variable in class org.jmol.script.Token
rotationAxis - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
rotationAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
rotationAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
rotationAxis - Variable in class etomica.models.nitrogen.TestRotationVector
rotationAxis - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
rotationAxis - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
rotationL - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
rotationM - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
rotationN - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
rotationradius - Static variable in class org.jmol.script.Token
rotationTensor - Variable in class etomica.association.BiasVolume2SiteAceticAcid
rotationTensor - Variable in class etomica.association.BiasVolumeAceticAcid
rotationTensor - Variable in class etomica.association.MCMoveBiasUBMolecule
rotationTensor - Variable in class etomica.association.MCMoveDimerRotate
rotationTensor - Variable in class etomica.association.MCMoveSmerRotate
rotationTensor - Variable in class etomica.data.meter.MeterKineticEnergyRigid
rotationTensor - Variable in class etomica.integrator.IntegratorRigidIterative
rotationTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
rotationTensor - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
rotationTensor - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
rotationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
rotationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
rotationTensor - Variable in class etomica.models.water.OrientationCalcWater3P
rotationTensor - Variable in class etomica.models.water.OrientationCalcWater4P
rotationTensor - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
rotationTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
RotationTensor - Interface in etomica.space: A tensor intended for use to define rotations in space.
rotationTensor - Variable in class etomica.space3d.OrientationFull3D
RotationTensor2D - Class in etomica.space2d
RotationTensor2D() - Constructor for class etomica.space2d.RotationTensor2D
rotationTensor3D - Variable in class etomica.models.water.P2Water4PSoft
RotationTensor3D - Class in etomica.space3d
RotationTensor3D() - Constructor for class etomica.space3d.RotationTensor3D
rotationTolerance - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
rotCounter - Variable in class etomica.dimer.IntegratorDimerMin
rotCounter - Variable in class etomica.dimer.IntegratorDimerRT
rotDim - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
rotNum - Variable in class etomica.dimer.IntegratorDimerRT
rotX(float) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to a rotation matrix about the x axis by the passed angle.
rotX(float) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to a rotation matrix about the x axis by the passed angle.
rotY(float) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to a rotation matrix about the y axis by the passed angle.
rotY(float) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to a rotation matrix about the y axis by the passed angle.
rotZ(float) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to a rotation matrix about the z axis by the passed angle.
rotZ(float) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to a rotation matrix about the z axis by the passed angle.
round(double) - Static method in class etomica.util.FastFourierTransform
roundInt(int) - Static method in class org.jmol.util.GData: JavaScript won't really have an integer here after integer division.
route - Variable in class etomica.action.IntegratorDimerApproach
routeParams - Variable in class etomica.action.IntegratorDimerApproach
rowHeaders - Variable in class etomica.data.types.DataTable.DataInfoTable
rowHeaders - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
rowLabelColumnHeader - Variable in class etomica.graphics.DisplayTable
rowLabels - Variable in class etomica.graphics.DisplayTable
rp - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
rPermutations - Variable in class etomica.virial.ClusterBonds
Rpol - Variable in class etomica.models.water.P2WaterSzalewicz
Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHe
Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
rPow - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
rPow - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
rPow - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
rPow - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
rr - Variable in class etomica.potential.P2HydrogenPatkowski
rr - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
rr0Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
rr0Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
rr0Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
rr0Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
rr1Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
rr1Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
rr1Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
rr1Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
rRand - Variable in class etomica.normalmode.MCMoveHarmonic
rrlong - Variable in class etomica.potential.P2HydrogenPatkowski
rrlong - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
rrounded - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
rScale - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
rScale - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
rScaled - Variable in class org.jmol.util.Rgb16
rTensor0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
rTensor0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
rTensor0 - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
rTensor0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
rTensor1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
rTensor1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
rTensor1 - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
rTensor1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
rTmp - Variable in class etomica.models.water.P2WaterSzalewicz
rTrial - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
rTrial - Variable in class etomica.virial.MCMoveClusterRingRegrow
rTrial - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
run() - Method in class etomica.action.activity.ActivityGroupParallel
run() - Method in class etomica.action.activity.ActivityGroupSeries: Causes uncompleted actions added to this group to be run in sequence.
run() - Method in class etomica.action.activity.ActivityIntegrate: Main loop for conduct of integration.
run() - Method in class etomica.action.activity.Controller: Causes uncompleted actions added to this group to be run in sequence.
run() - Method in class etomica.action.Activity: Method defining the behavior of the activity.
run(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
run() - Method in class etomica.graph.engine.Launcher.ConsoleWindowRunnable
run() - Method in class etomica.threaded.atom.PotentialMasterListWorker
run() - Method in class etomica.threaded.domain.PotentialMasterListWorker
run() - Method in class etomica.threads.ThreadsMD
run() - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
run() - Method in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
run() - Method in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
runBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
runBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
runEmul() - Method in class etomica.potential.PotentialEmul
rungeKutta4(int, double, OdeSolver.Variables, OdeSolver.Rhs) - Static method in class etomica.util.OdeSolver: Performs Runge-Kutta integration for fixed number of constant-sized steps.
rungeKuttaAdaptive(OdeSolver.Variables, double, double, OdeSolver.Rhs) - Static method in class etomica.util.OdeSolver: Runge-Kutta integration using an adaptive step-size.
runGraphic(SimulationVirialOverlap2, int, DisplayTextBox, DisplayTextBox, IAction) - Method in class etomica.virial.GUI.components.SimulationRunner
runit() - Method in class etomica.models.hexane.TestSetToUHexane
runMD() - Method in class etomica.threads.AtomDecompositionMD
runName - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
runName - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
runName - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
running - Variable in class etomica.modules.clustergenerator.MyApplet
runQChem() - Method in class etomica.potential.P2QChem
runSimulation(ModelSimulationEnvironment, ArrayList<ICollectionPotential>) - Method in class etomica.virial.GUI.components.SimulationRunner
runVirial(VirialExternalFieldConfinedOverlap.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
runVirial(VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
runVirial(VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
runVirial(VirialExternalFieldOverlapRho.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldOverlapRho
runVirial(VirialLJ.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJ
runVirial(VirialLJSeries.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJSeries
runVirial(VirialSW.VirialSWParam) - Static method in class etomica.virial.simulations.VirialSW
rv - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
rv - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
Rvdw - Static variable in class etomica.potential.P2QChemInterpolated
RvdwF - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
RvdwF - Variable in class etomica.potential.P2QChemInterpolated
RvdwF - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
RvdwF - Variable in class etomica.potential.P3QChem.DampingParams
RYDBERG_R - Static variable in class etomica.util.Constants: Rydberg's constant, in Angstroms.
rzero - Variable in class etomica.dimer.P1LepsHarmonic

S

S - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
s - Static variable in class etomica.models.water.P2WaterTIP4P
s - Variable in class etomica.modules.rheology.IntegratorPolymer
s - Static variable in class etomica.potential.P2O2Bartolomei
s - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
s - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
s - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
s - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
s - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
s - Variable in class g3dsys.images.Line
S1DHR(int, double, int) - Static method in class etomica.normalmode.NormalModes1DHR: Returns the analytical result for the S matrix (just a scalar in this case) for the 1D HR system with PBC
S2 - Variable in class etomica.models.water.P2WaterSzalewicz
S2fit(double, double, double, double, double, double, double) - Method in class etomica.models.water.P2WaterSzalewicz
S3 - Variable in class etomica.models.water.P2WaterSzalewicz
sa - Static variable in class etomica.potential.P2WaterPotentialsJankowski
saa - Static variable in class etomica.potential.P2O2Bartolomei
saaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
saaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
saddle - Variable in class etomica.dimer.IntegratorDimerMin
saddle - Variable in class etomica.dimer.SimDimerLJadatom
saddle - Variable in class etomica.dimer.SimDimerLJgb
saddle - Variable in class etomica.dimer.SimDimerMEAMadatom
saddle - Variable in class etomica.dimer.SimDimerMEAMGB
saddleEnergy - Variable in class etomica.dimer.IntegratorDimerRT
saddleFine - Variable in class etomica.dimer.SimDimerLJadatom
saddleFound - Variable in class etomica.dimer.IntegratorDimerRT
saddleT - Variable in class etomica.dimer.IntegratorDimerRT
safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.AbstractOptionHandler
safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
safetl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
safeTruncate(float, int) - Static method in class org.jmol.util.TextFormat
safetyFactor - Variable in class etomica.nbr.CriterionPositionWall
safetyFactor - Variable in class etomica.nbr.CriterionSimple
safetyFactor - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
sajmols - Static variable in class etomica.potential.P2O2Bartolomei
sajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
sajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
sajp1 - Static variable in class etomica.potential.P2O2Bartolomei
sajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
sajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
sajpn - Static variable in class etomica.potential.P2O2Bartolomei
sajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
sajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
Sam - Class in etomica.modules.sam: Self-assembled monolayer module.
Sam() - Constructor for class etomica.modules.sam.Sam
SamGraphic - Class in etomica.modules.sam
SamGraphic(Sam) - Constructor for class etomica.modules.sam.SamGraphic
SamGraphic.ActionMoveWall - Class in etomica.modules.sam
SamGraphic.Applet - Class in etomica.modules.sam
SamGraphic.DataPipeStressStrain - Class in etomica.modules.sam
SamGraphic.ModifierWallPosition - Class in etomica.modules.sam
sampleCluster - Variable in class etomica.virial.BoxCluster
sampleCluster - Variable in class etomica.virial.simulations.SimulationVirial
sampleCluster - Variable in class etomica.virial.simulations.SimulationVirialPT
sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap
sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
sampleCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
sampleCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
sampleCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
sanityCheckBC - Variable in class etomica.data.AccumulatorAverageFixed
sasurface - Static variable in class org.jmol.script.Token
satisfies(Requirement) - Method in class etomica.compatibility.FeatureSet
save(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
save - Static variable in class org.jmol.script.Token
savedSeed - Variable in class etomica.util.RandomMersenneTwister
savedSeedArray - Variable in class etomica.util.RandomMersenneTwister
saveproteinstructurestate - Static variable in class org.jmol.script.Token
saveValues - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
sb - Static variable in class etomica.potential.P2WaterPotentialsJankowski
sbet - Static variable in class etomica.potential.P2O2Bartolomei
sbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
sbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
sBOType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
scale - Variable in class etomica.graphics.DisplayBox: Factor used to scale the size of the image.
scale - Variable in class etomica.graphics.DisplayPolytope: Factor used to scale the size of the image.
scale - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
scale - Variable in class etomica.virial.MCMoveClusterRingScale
scale - Variable in class org.jmol.util.Quadric
scale(float) - Method in class org.jmol.util.Quadric
scale(float) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the scalar multiplication of itself.
scale(float) - Method in class org.jmol.util.Tuple4f: Sets the value of this tuple to the scalar multiplication of itself.
scaleAdd(float, Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the scalar multiplication of itself and then adds tuple t1 (this = s*this + t1).
scaleAdd(int, Tuple3i, Tuple3i) - Method in class org.jmol.util.Tuple3i: Sets the value of this tuple to the scalar multiplication of tuple t1 plus tuple t2 (this = s*t1 + t2).
scaleAdd2(float, Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).
scaleangstromsperinch - Static variable in class org.jmol.script.Token
scaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociated
scaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
scaleBox(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
scaleBy(double) - Method in class etomica.lattice.LatticeCubicBcc: Rescales the lattice by the given factor.
scaleBy(double) - Method in class etomica.lattice.LatticeCubicDiamond: Rescales the lattice by the given factor.
scaleBy(double) - Method in class etomica.lattice.LatticeCubicFcc: Rescales the lattice by the given factor.
scaleBy(double) - Method in class etomica.lattice.LatticeCubicSimple: Rescales the lattice by the given factor.
scaleBy(double) - Method in class etomica.lattice.LatticeHcp: Rescales the lattice by the given factor.
scaleBy(double) - Method in class etomica.lattice.LatticeOrthorhombicHexagonal: Rescales the lattice by the given factor.
scaleFitToScreen() - Method in class g3dsys.control.G3DSys
scaleMomenta() - Method in class etomica.integrator.IntegratorHard: Updates collision times appropriately after scaling momenta.
scaleMomenta() - Method in class etomica.integrator.IntegratorMD: Crude method to enforce constant-temperature constraint Scales momenta of all atoms by a constant factor so that box adheres to setpoint temperature.
scaleMomenta(IVector) - Method in class etomica.integrator.IntegratorMD
scaleMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
scaleMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
scaleMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
scalePixelsPerAngstrom - Variable in class g3dsys.control.TransformManager
scalePrec(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Append decimal zeros to the value.
scalePrec(BigComplex, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Append decimal zeros to the value.
scalePrec(BigDecimal, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Boost the precision by appending decimal zeros to the value.
scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvas1D: Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvas2D: Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) - Method in class etomica.graphics.DisplayPolytopeCanvas2D: Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSetSize(int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins: Sets the size of the display to a new value and scales the image so that the box fits in the canvas in the same proportion as before.
scaleSize(double) - Method in class etomica.lattice.crystal.Primitive: Scales (multiplies) the size of each primitive vector by the given value.
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveBcc: Multiplies the size of the current vectors by the given value.
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveCubic
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveFcc: Multiplies the size of the current vectors by the given value.
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveGeneral
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
scaleSize(double) - Method in class etomica.models.hexane.PrimitiveHexane
scaleSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
scaleVector - Variable in class etomica.action.BoxInflate
scaleVector - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
scaleVector - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
scaling - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
scaling - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
scBeads - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
scf - Variable in class etomica.potential.P2QChemInterpolated
scf - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
scfAtoms - Variable in class etomica.virial.ClusterSumPolarizable
scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
ScientificFormat - Class in etomica.util: a formatter that uses a format suitable for numeric values in a scientific context.
ScientificFormat() - Constructor for class etomica.util.ScientificFormat: Create a ScientificFormat using the default pattern and symbols for the default locale.
ScientificFormat(Locale) - Constructor for class etomica.util.ScientificFormat: Create a ScientificFormat using the default pattern for the given locale.
ScientificFormat(String) - Constructor for class etomica.util.ScientificFormat: Creates a ScientificFormat using a given pattern
ScientificFormat(Locale, String) - Constructor for class etomica.util.ScientificFormat: Creates a ScientificFormat using a given pattern for the specified locale
scoreGreaterThan(int[]) - Method in class etomica.virial.cluster.ClusterDiagram: Determines if the cluster's current configuration has a score greater than the given score.
screenDiameter - Variable in class org.jmol.util.Point3fi
screened - Variable in class etomica.virial.ClusterWheatleyHS
screened - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
screenSpace(Point3f, Point3i) - Method in class g3dsys.control.G3DSys: Converts molspace point p (in Angstroms) to a point on the display in pixels.
screenx - Static variable in class org.jmol.script.Token
screenX - Variable in class org.jmol.util.Point3fi
screenxyz - Static variable in class org.jmol.script.Token
screeny - Static variable in class org.jmol.script.Token
screenY - Variable in class org.jmol.util.Point3fi
screenz - Static variable in class org.jmol.script.Token
screenZ - Variable in class org.jmol.util.Point3fi
SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JmolConstants
scriptCommand - Static variable in class org.jmol.script.Token
scriptqueue - Static variable in class org.jmol.script.Token
scriptreportinglevel - Static variable in class org.jmol.script.Token
ScriptVariable - Class in org.jmol.script
ScriptVariable(int) - Constructor for class org.jmol.script.ScriptVariable
ScriptVariable.Sort - Class in org.jmol.script
ScriptVariableInt - Class in org.jmol.script
ScriptVariableInt(int) - Constructor for class org.jmol.script.ScriptVariableInt
SearchState - Interface in etomica.graph.isomorphism
secDerXr - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
secDerXr - Variable in class etomica.models.nitrogen.P2Nitrogen
Second - Class in etomica.units
secondaryBox - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
secondaryBox - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
secondaryCoordDef - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
secondaryCoordDef - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
secondaryDirection - Variable in class etomica.config.ConfigurationOrientedFile
secondaryDirection - Variable in class etomica.space3d.OrientationFull3D
secondAxis - Variable in class etomica.association.BiasVolume2SiteAceticAcid
secondAxis - Variable in class etomica.association.BiasVolumeAceticAcid
secondBox - Variable in class etomica.integrator.mcmove.MCMoveVolumeExchange
secondder - Variable in class etomica.meam.PotentialCuLREP
secondder(IAtomList) - Method in class etomica.meam.PotentialCuLREP
secondder - Variable in class etomica.meam.PotentialEFS
secondder(IAtomList) - Method in class etomica.meam.PotentialEFS
secondder - Variable in class etomica.meam.PotentialFeEAM
secondder(IAtomList) - Method in class etomica.meam.PotentialFeEAM
secondder - Variable in class etomica.meam.PotentialFeEAM_LS
secondDerivative(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
secondDerivative - Variable in class etomica.models.water.P2Water4PSoft
secondDerivative(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
secondDerivative - Variable in class etomica.potential.EwaldSummation
secondDerivative(IAtom, IAtom) - Method in class etomica.potential.EwaldSummation
secondDerivative(IMoleculeList) - Method in interface etomica.potential.IPotentialMolecularSecondDerivative
secondDerivative - Variable in class etomica.potential.P2HSDipole
secondDerivative(IMoleculeList) - Method in class etomica.potential.P2HSDipole
secondDerivative - Variable in class etomica.potential.P2LJDipole
secondDerivative(IMoleculeList) - Method in class etomica.potential.P2LJDipole
secondDerivative - Variable in class etomica.potential.P2ReactionFieldDipole
secondDerivative(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
secondDerivativeSum - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
secondDerivativeSum - Variable in class etomica.potential.PotentialCalculationPhiSum
secondDerivativeXr(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
secondDerivativeXrRotRot(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
securityOff - Variable in class etomica.graph.view.rasterizer.SVGConverter: Controls whether scripts should be run securely or not
seed - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
seeds - Variable in class etomica.simulation.Simulation
seen(byte) - Method in class etomica.graph.traversal.AbstractTraversal
seenAll() - Method in class etomica.graph.traversal.AbstractTraversal
seenArrays - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
seenParams - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
segment - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
segmentList - Variable in class etomica.graph.property.FFTDecomposition
selectallmodels - Static variable in class org.jmol.script.Token
selected - Static variable in class org.jmol.script.Token
selectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
selectedAtoms - Variable in class etomica.virial.MCMoveClusterRotateCH3
selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleMulti
selectedfloat - Static variable in class org.jmol.script.Token
selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionMulti
selecthetero - Static variable in class org.jmol.script.Token
selecthydrogen - Static variable in class org.jmol.script.Token
selectionForKey(char, ComboBoxModel) - Method in class etomica.graphics.DimensionedDoubleEditor: Implementation of KeySelectionManager interface that uses key press to select a unit prefix (instead of selecting a combo box item).
selectionhalos - Static variable in class org.jmol.script.Token
selectItemTok(Token) - Static method in class org.jmol.script.ScriptVariable
selectItemTok(Token, int) - Static method in class org.jmol.script.ScriptVariable
selectItemVar(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
selectItemVar2(ScriptVariable, int) - Static method in class org.jmol.script.ScriptVariable
selectMolecules() - Method in class etomica.virial.MCMoveClusterReptateMulti
selectMolecules() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
selectMolecules() - Method in class etomica.virial.MCMoveClusterTorsionMulti
selectMove() - Method in class etomica.integrator.mcmove.MCMoveManager: Selects a MCMove instance from among those added to the integrator, with probability in proportion to the frequency value assigned to the move.
selfELJ - Static variable in class etomica.models.clathrates.MinimizationTIP4P
semiClassical - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
semiClassical - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
semiClassical - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
semiClassical - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
semiClassical - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
sep - Variable in class etomica.models.water.P2WaterSzalewicz
separationProbability(int, double) - Static method in class etomica.virial.MCMoveClusterAtomHSRing: Normalized probability for the separation of the centers of two spheres located at the end of a chain of (n+1) overlapping spheres.
seq - Variable in class etomica.virial.MCMoveClusterAtomHSChain
seq - Variable in class etomica.virial.MCMoveClusterAtomHSRing
seq - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
sequence - Static variable in class org.jmol.script.Token
serial - Variable in class etomica.modules.droplet.EllipseDisplayAction
serialVersionUID - Static variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
serialVersionUID - Static variable in class etomica.models.rowley.DimerApproach
set(int, IAtom) - Method in class etomica.atom.AtomArrayList
set(int, IMolecule) - Method in class etomica.atom.MoleculeArrayList
set(Parser.CommandPropertyValue) - Method in class etomica.graph.engine.Interpreter
set(int, Object) - Method in class etomica.util.ObjectArrayList: Replaces the element at the specified position in this list with the specified element.
set(int, Rational) - Method in class etomica.veos.bigdecimal.Bernoulli: Set a coefficient in the internal table.
set(int, BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Set a polynomial coefficient.
set(int, int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Set a polynomial coefficient.
set(int) - Method in class etomica.veos.bigdecimal.Euler: Compute a coefficient in the internal table.
set(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptVariable: creates a NEW version of the variable
set(int) - Method in class org.jmol.util.BitSet: Sets the bit at the specified index to true.
set(Quaternion) - Method in class org.jmol.util.Quaternion
set(float, float, float) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the specified xyz coordinates.
set(int, int, int) - Method in class org.jmol.util.Tuple3i: Sets the value of this tuple to to the specified x, y, and z coordinates.
set(float, float, float, float) - Method in class org.jmol.util.Tuple4f: Sets the value of this tuple to the specified xyzw coordinates.
set2(Point3f, Point3i) - Static method in class org.jmol.util.Point3fi
set4(float, float, float, float) - Method in class org.jmol.util.AxisAngle4f: Sets the value of this axis angle to the specified x,y,z,angle.
set_sites(IVector[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
set_sites_itypea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
set_sites_sa - Static variable in class etomica.potential.P2WaterPotentialsJankowski
set_sites_sitea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
setA(double) - Method in class etomica.models.hexane.PrimitiveHexane: Sets A and scales B and C to maintain relative size
setA(double) - Method in class etomica.modules.rheology.IntegratorPolymer
setA(double) - Method in class etomica.potential.P2Exp6
setA(int, double) - Method in class etomica.potential.P2HeSimplified: Sets the ith parameter value u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X where X = 10 if useC10 is true, X=8 otherwise
setA(double) - Method in class etomica.potential.P2ModifiedMorse
setA(double) - Method in class etomica.potential.P2Morse
setA() - Method in class etomica.potential.P3CPSNonAdditiveHe
setA() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setA(float[]) - Method in class org.jmol.util.Matrix3f: Sets the values in this Matrix3f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
setA(float[]) - Method in class org.jmol.util.Matrix4f: Sets the values in this Matrix4f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).
setA(float[]) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple from the 3 values specified in the array.
setAA(AxisAngle4f) - Method in class org.jmol.util.AxisAngle4f: Sets the value of this axis angle to the value of axis angle t1.
setAA(AxisAngle4f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.
setAA(AxisAngle4f) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.
setAA(AxisAngle4f) - Method in class org.jmol.util.Quaternion
setABC(int) - Method in class org.jmol.util.MeshSurface
setAcceptanceTarget(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker: Sets the desired rate of acceptance (as a fraction between 0 and 1 inclusive) of trials of this move.
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
setAccumulator(AccumulatorAverage) - Method in class etomica.graphics.DisplayTextBoxesCAE: Specifies the accumulator that generates the displayed values.
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorVar
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlap
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapLJ
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphere
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSSnxy
setAccumulator(IDataSink) - Method in class etomica.virial.simulations.SimulationVirial
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
setAccumulator(int, DataAccumulator) - Method in class etomica.virial.simulations.SimulationVirialPT
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirial
setAccumulatorBlockSize(int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setAccumulators(AccumulatorAverageCollapsingLog[]) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
setAccumulatorUpdateInterval(int) - Method in class etomica.data.DataTableAverages: Sets the interval for updates to the accumulators feeding this table.
setAction(IAction) - Method in class etomica.graphics.DeviceButton: Defines the action to be performed when the button is pressed.
setAction(IntegratorAnalytic.AtomTimeAction) - Method in class etomica.integrator.IntegratorAnalytic
setAction(IAction) - Method in class etomica.zeolite.DeviceButtonSingle: Defines the action to be performed when the button is pressed.
setActions(IAction[]) - Method in class etomica.action.activity.ActivityGroupParallel
setActive(boolean) - Method in class etomica.data.DataAccumulator: Sets whether accumulation is to be performed in response to interval events.
setActive(int, boolean, boolean) - Method in class etomica.potential.P1HardBoundary
setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger: Changes the activation state for a logging level.
setActivityIntegrate(ActivityIntegrate) - Method in class etomica.dimer.IntegratorDimerMin
setActivityIntegrate(ActivityIntegrate) - Method in class etomica.dimer.IntegratorDimerRT
setAddAnotherSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAddPotential(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAddPotential(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setAddSameSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAddSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAddSpecies1(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAddSpecies2(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAddSpecies3(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAdiabatic() - Method in class etomica.graphics.DeviceThermoSlider: Set the Adiabatic button to its selected state.
setAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the Adiabatic button to its selected state.
setAdjustInterval(long) - Method in class etomica.integrator.mcmove.MCMoveStepTracker: Sets the interval between steps size adjustments.
setAdjustInterval(long) - Method in class etomica.overlap.IntegratorOverlap: Sets how frequently the appropriate reference vs.
setAdjustStepFraction(boolean) - Method in class etomica.overlap.IntegratorOverlap: Sets whether to adjust the number of relative number of steps for each sub-integrator.
setAdjustStepFreq(boolean) - Method in class etomica.virial.overlap.IntegratorOverlap: Sets whether to adjust the number of relative number of steps for each sub-integrator.
setAdjustStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker: Sets the step adjustment size.
setAelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setAgent(IAtom, E) - Method in class etomica.atom.AtomLeafAgentManager: Sets the agent associated with the given atom to be the given agent.
setAgent(IAtomType, Object) - Method in class etomica.atom.AtomTypeAgentManager: Sets the agent associated with the given atom type to be the given agent.
setAgent(IMolecule, Object) - Method in class etomica.atom.MoleculeAgentManager: Sets the agent associated with the given atom to be the given agent.
setAgent(ISpecies, Object) - Method in class etomica.atom.SpeciesAgentManager: Sets the agent associated with the given atom type to be the given agent.
setAgent(IBox, E) - Method in class etomica.box.BoxAgentManager
setAgentManager(AtomLeafAgentManager<IntegratorHard.Agent>) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
setAgentManager(AtomLeafAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
setAgentManager(AtomLeafAgentManager<AtomPotentialList>) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
setAgentManager(AtomLeafAgentManager<? extends Integrator.Forcible>) - Method in class etomica.potential.PotentialCalculationForceSum
setAgentManager(AtomLeafAgentManager) - Method in class etomica.potential.PotentialCalculationTorqueSum
setAgentManager(AtomLeafAgentManager<? extends Integrator.Forcible>) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
setAggressiveAdjustStepFraction(boolean) - Method in class etomica.overlap.IntegratorOverlap: Sets whether to use "aggressive" adjustment.
setAlertMessage(String) - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
setAlertMsgBoxController(ControllerAlertMsgBox) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
setAlertMsgBoxSpeciesRemoval(ViewAlertMsgBoxSpeciesRemoval) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setAlign(int, int) - Method in class etomica.graphics.DisplayBox
setAlign(int, int) - Method in class etomica.graphics.DisplayPolytope
setAlkaneIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setAlkaneIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setAlkaneLength(int, int) - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
setAlkaneLengthSelectionDM(ModelAlkaneLengthSelection) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
setAlkaneLengthSelectionView(ViewAlkaneLengthSelection, int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
setAll(int) - Static method in class org.jmol.util.BitSetUtil
setAllEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the "All eigenvalues" button to its selected state.
setAllowedScriptTypes(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the set of allowed script types (i.e., the set of possible values for the type attribute in the <script> element), as a comma separated list of allowed values.
setAllowEqualElements(boolean) - Method in class etomica.lattice.IndexIteratorTriangular: Sets flag indicating whether iterates may have elements that are equal to one another.
setAllPermutations(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to generate all permutations.
setAllPermutations(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setAllPermutations(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setAllUnits(Unit) - Method in class etomica.graphics.DisplayTable: Sets the units of all columns to the given unit.
setAllWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the "All Wave Vectors" button to its selected state.
setAlpha(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
setAlpha(double[]) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setAlpha(double[]) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setAlpha(double[], double[]) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR: sets the range of parameter values used for Bennets method.
setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
setAlpha(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
setAlpha(double[]) - Method in class etomica.normalmode.MeterOverlapSwitch
setAlpha(double[]) - Method in class etomica.normalmode.MeterTargetTP
setAlpha(double, double) - Method in class etomica.normalmode.SimOverlapModule
setAlpha(double) - Method in class etomica.potential.P2Dreiding
setAlpha(double) - Method in class etomica.potential.P2Exp6Buckingham
setAlpha() - Method in class etomica.potential.P3CPSNonAdditiveHe
setAlpha() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setAlphaCenter(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
setAlphaEin(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal: Sets the Einstein spring constant u = alpha * r^2
setAlphaEin(double) - Method in class etomica.normalmode.MCMoveHarmonicEin: Sets the Einstein spring constant
setAlphaFac(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
setAlphaRange(double, double) - Method in class etomica.overlap.MeterOverlap: sets the range of parameter values used for Bennets method.
setAlphaSpan(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setAlphaSpan(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setAlphaSpan(double) - Method in class etomica.normalmode.MeterOverlapSwitch
setAlphaSpan(double) - Method in class etomica.normalmode.MeterTargetTP
setAlternateStylesheet(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the alternateStyleSheet value.
setAlterSimEnv(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setAlterSimEnv(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setAmbientPercent(int) - Static method in class org.jmol.util.GData: fractional distance from black for ambient color
setAmplitude(double) - Method in class etomica.potential.P2Fene
setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
setAngle(int, double) - Method in class etomica.config.ConformationChainLinear
setAngle(int, double) - Method in class etomica.config.ConformationLinear
setAngle(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setAngle(double) - Method in class etomica.potential.P3BondAngle: Sets the nominal bond angle (in radians)
setAngle(double) - Method in class etomica.potential.P3BondAngleDreiding: Sets the nominal bond angle (in radians)
setAngle(double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig: Sets the nominal bond angle (in radians)
setAngleAlpha(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
setAngleBeta(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
setAngleBeta(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
setAngleGamma(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
setAngles(double, double, double) - Method in class etomica.action.AtomActionRotateBy
setAngles(double[]) - Method in class etomica.lattice.crystal.Primitive: Sets the angles between the primitive vector to the corresponding values in the given array.
setAngles(double[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
setAnharmonicConstant(double) - Method in class etomica.potential.P2Anharmonic
setAppending(boolean) - Method in class etomica.data.DataLogger: Overwrite or attach the data to the file.
setApplyToMolecules(boolean) - Method in class etomica.action.BoxImposePbc: Sets a flag indicating whether periodic boundaries are applied to the molecules (true), or to the atoms (false).
setApproximation(int) - Method in class etomica.virial.cluster.ClusterOperations
setArea(Rectangle2D) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the area as a Rectangle.
setArray(double[][]) - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
setArrayList(AtomArrayList) - Method in class etomica.atom.AtomToAtomSetFixed
setArrayList(MoleculeArrayList) - Method in class etomica.atom.MoleculeToMoleculeSetFixed
setArrayListPotentialCollection(ArrayList<ICollectionPotential>) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
setArrayShape(int[]) - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory: Sets the array shape.
setArrayShape(int[]) - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory: Sets the array shape.
setAsCube(double) - Method in class etomica.space.BoundaryDeformablePeriodic: Sets the shape of the boundary to a cube with edges equal to the given value.
setAspect(float) - Method in class g3dsys.images.Ellipse
setAsRectangular(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic: Sets the shape of the boundary as a rectangular parallelepiped (or parallelogram) with edge lengths given by the elements of the given vector.
setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomDimer
setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomMonomer
setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomSmer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomDimer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomMonomer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomNoSmer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomSmer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveBiasUB
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveBiasUBMolecule
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveDimer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveDimerRotate
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeMonomer
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeRotateAssociated
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeSmer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveRotateAssociated
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveRotateNoSmer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveSmer
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveSmerRotate
setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveVolumeAssociated
setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
setAssociationManager(AssociationManager) - Method in class etomica.association.MeterDimerMoleFraction
setAssociationManager(AssociationManagerMolecule) - Method in class etomica.association.MoleculeSourceRandomDimer
setAssociationManager(AssociationManagerMolecule) - Method in class etomica.association.MoleculeSourceRandomMonomer
setAsText(String) - Method in class etomica.graphics.DimensionedDoubleEditor: Sets the value, interpreted as being in the editor's units, from a text string.
setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorArrayList: Sets the first atom for iteration.
setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Sets the first atom for iteration.
setAtom(IAtom) - Method in interface etomica.atom.iterator.AtomIteratorAtomDependent
setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorSinglet: Defines atom returned by iterator and leaves iterator unset.
setAtom(IAtom) - Method in class etomica.graphics.ColorSchemeNeighbor
setAtom(IAtom) - Method in class etomica.graphics.ColorSchemeNeighborCell
setAtom(IAtom) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp: sets the atom whose collision time is to be calculated
setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
setAtom(IAtom) - Method in class etomica.nbr.site.AtomSite
setAtomAgentManager(IBox, AtomLeafAgentManager<? extends IVector>) - Method in class etomica.potential.P1HarmonicSite
setAtomFilter(AtomFilter) - Method in class etomica.graphics.DisplayBox: Mutator method for the atom filter that determines which atoms are displayed.
setAtomInfo(IAtomType, P2SemiclassicalAtomic.AtomInfo) - Method in class etomica.potential.P2SemiclassicalAtomic
setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterElongation
setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterStrain
setAtomPositionDefinition(IAtomPositionDefinition) - Method in class etomica.action.MoleculeActionTranslateTo
setAtomPositionDefinition(IAtomPositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
setAtomPositionDefinition(IAtomPositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
setAtoms(IAtomList) - Method in class etomica.atom.AtomListWrapper: Copies the atoms in the given atom set to the wrapped array of atoms.
setAtoms(IAtom[]) - Method in class etomica.atom.AtomsetArray: Copies the atoms in the given array to the wrapped, final array of atoms.
setAtoms(IAtomList) - Method in class etomica.atom.AtomsetArray: Copies the atoms in the given atom set to the wrapped array of atoms.
setAtoms(IMoleculeList) - Method in class etomica.atom.MoleculeListWrapper: Copies the atoms in the given atom set to the wrapped array of atoms.
setAtoms(IMolecule[]) - Method in class etomica.atom.MoleculesetArray: Copies the atoms in the given array to the wrapped, final array of atoms.
setAtoms(IMoleculeList) - Method in class etomica.atom.MoleculesetArray: Copies the atoms in the given atom set to the wrapped array of atoms.
setAtoms(IAtom, IAtom) - Method in class etomica.data.DataSourceAtomDistance
setAtoms(IMoleculeList) - Method in class etomica.data.meter.MeterStructureFactor
setAtomSource(AtomSource) - Method in class etomica.association.MCMoveDimer
setAtomSource(AtomSource) - Method in class etomica.association.MCMoveDimerRotate
setAtomSource(AtomSource) - Method in class etomica.association.MCMoveSmer
setAtomSource(AtomSource) - Method in class etomica.association.MCMoveSmerRotate
setAtomSource(AtomSource) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
setAtomSource(AtomSource) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveAtom
setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveDimer
setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
setAtomSource(MoleculeSource) - Method in class etomica.models.hexane.MCMoveReptate
setAtomSource(AtomSource) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupled
setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
setAtomSource(AtomSource) - Method in class etomica.virial.MCMoveClusterAtomQ
setAtomType(IAtomType) - Method in class etomica.data.meter.MeterRDF
setAtomType(IAtomType) - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
setAtomTypes(IAtomType, IAtomType) - Method in class etomica.data.meter.MeterRDF
setAtomTypes(int[]) - Method in class etomica.species.SpeciesSpheresCustom
setAutoScale(boolean) - Method in class etomica.graphics.DevicePlotPoints
setAvgDef(boolean) - Method in class etomica.normalmode.DataSourceFE
setAxial(int, double) - Method in interface etomica.space.RotationTensor
setAxial(int, double) - Method in class etomica.space2d.RotationTensor2D
setAxial(int, double) - Method in class etomica.space3d.RotationTensor3D: Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by the given angle.
setAxisSymmetric(boolean) - Method in class etomica.species.SpeciesSpheresRotating
setB(double) - Method in class etomica.modules.rheology.IntegratorPolymer
setB(double) - Method in class etomica.modules.sam.P1Sinusoidal
setB(double) - Method in class etomica.potential.P2Exp6
setBackgroundArgb(int) - Method in class org.jmol.util.GData: sets background color to the specified argb value
setBackgroundColor(Color) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the backgroundColor value.
setBackgroundColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Sets the background color of the display box canvas.
setBackgroundColor(Color) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Sets the background color of the display box canvas.
setBackgroundImage(Object) - Method in class org.jmol.util.GData
setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
setBarrier(double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntergroupCoupled: Specifies the basis, which identifies the molecules subject to iteration.
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntergroupExchange: Specifies the basis, which identifies the molecules subject to iteration.
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntragroupExchange: Specifies the basis, which identifies the molecules subject to iteration.
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIndexList
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntergroup: Specifies the basis, which identifies the atoms subject to iteration.
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntergroupExchange
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntragroup: Specifies the parent atom of the iterates.
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomIteratorBasis: Sets the basis for iteration, such that the childList atoms of the given atom will be subject to iteration (within any specifications given by a prior or subsequent call to setTarget).
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart: Sets the basis for iteration, such that the childList atoms of the given atom will be subject to iteration (within any specifications given by a prior or subsequent call to setTarget).
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
setBasis(IMoleculeList) - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent: Identifies the atoms that form the basis for iteration, such that the childList atoms of those given will form the iterates.
setBasis(IMoleculeList) - Method in interface etomica.atom.iterator.MoleculesetIteratorBasisDependent
setBasis(IMoleculeList) - Method in class etomica.atom.iterator.TripletInnerSequential
setBasis(IMoleculeList) - Method in class etomica.potential.PotentialMaster.AtomIterator0
setBasisMolecules(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
setBasisMonoclinic() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
setBasisOrthorhombic() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
setBasisSurface(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
setBbcage(float) - Method in class org.jmol.util.BoxInfo
setBennetParam(double, double) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2: sets the range of parameter values used for Bennets method.
setBennetParam(double, double) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage: sets the range of parameter values used for Bennets method.
setBennetParam(double, double) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap: sets the range of parameter values used for Bennets method.
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
setBeta(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
setBeta(double) - Method in class etomica.potential.P4TorsionDreiding
setBeta3() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setBeta4211() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setBeta4220() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setBetaPhase(boolean) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setBetaPositionAndOrientation(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setBGColor(Color) - Method in class g3dsys.control.G3DSys: Change the background color of the G3D display
setBiasCubeDimensions(IVector) - Method in class etomica.association.BiasVolumeCube
setBiasCubeDimensions(double) - Method in class etomica.association.BiasVolumeCube
setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeAceticAcid
setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphere
setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphereOriented
setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
setBiasSphereRadius(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeAceticAcid
setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphere
setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphereOriented
setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
setBiasVolume(BiasVolume2SiteAceticAcid) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
setBiasVolume(BiasVolume2SiteAceticAcid) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
setBinSize(double) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
setBit(int) - Method in interface etomica.graph.model.Bitmap
setBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong: The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit bitSize() - 1 of bitmap.
setBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector: The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit bitSize() - 1 of bitmap[size()-1].
setBits(boolean) - Method in interface etomica.graph.model.Bitmap
setBits(boolean) - Method in class etomica.graph.model.impl.AbstractBitmap
setBits(boolean) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1).
setBits(boolean) - Method in class etomica.graph.model.impl.BitmapOfLongVector
setBits(int, int) - Method in class org.jmol.util.BitSet: Sets the bits from the specified fromIndex (inclusive) to the specified toIndex (exclusive) to true.
setBitSize(int) - Method in class etomica.graph.model.impl.BitmapOfLong
setBitSize(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
setBitTo(int, boolean) - Method in class org.jmol.util.BitSet: Sets the bit at the specified index to the specified value.
setBlockDataSink(IDataSink) - Method in class etomica.data.AccumulatorAverageFixed
setBlockSize(long) - Method in class etomica.data.AccumulatorAverage: Sets the size of the block used to group data for error analysis.
setBlockSize(long) - Method in class etomica.data.AccumulatorAverageCollapsing: Sets the size of the block used to group data for error analysis.
setBondConstraints(ISpecies, int[][], double[]) - Method in class etomica.integrator.IntegratorVelocityVerletShake
setBondDelta(double) - Method in class etomica.potential.P2HardBond: Sets the bond extension factor (max = length * (1+delta))
setBondDelta(double) - Method in class etomica.potential.P2PenetrableBond: Sets the bond extension factor (max = length * (1+delta))
setBonded(boolean) - Method in class etomica.nbr.CriterionBondedSimple
setBonded(boolean, IAtom, IAtom, double) - Method in class etomica.potential.P2HardBondedList: Adds/removes the pair of atoms to/from each other's bonded list.
setBondedSurfaceAtoms(IMolecule, IAtomList) - Method in class etomica.modules.sam.CriterionTether3
setBondFac(double) - Method in class etomica.modules.colloid.P2HardSphereMC
setBondFac(double) - Method in class etomica.modules.colloid.P2SquareWellMonomer
setBondingPotential(Potential2) - Method in class etomica.chem.models.ModelChain: Set the bonding potential for adjacent atoms in the chain molecule.
setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
setBondL(double) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
setBondL(double) - Method in class etomica.virial.SpeciesFactorySpheres2
setBondLength(double) - Method in class etomica.atom.AtomHydrogen
setBondLength(double) - Method in class etomica.config.ConformationChainLinear
setBondLength(double) - Method in class etomica.config.ConformationLinear
setBondLength(double) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
setBondLength(double) - Method in class etomica.potential.P2Dreiding
setBondLength(double) - Method in class etomica.potential.P2HardBond: Setter method for the bond length
setBondLength(double) - Method in class etomica.potential.P2PenetrableBond: Setter method for the bond length
setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setBondLength(double) - Method in class etomica.virial.MCMoveClusterReptateMulti
setBondLength(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
setBondLength(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
setBondLengths(double[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
setBonds(int[][]) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
setBonds(int[]) - Method in class etomica.virial.cluster.ClusterTreeNode
setBondTheta(double) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
setBondTheta(double) - Method in class etomica.virial.SpeciesFactorySpheres2
setBondType(int) - Method in class etomica.models.water.P2HardAssociationGCPMReference
setBondType(int) - Method in class etomica.models.water.PNWaterGCPMThreeSite
setBondType(int) - Method in class g3dsys.images.Bond
setBoolean(boolean) - Method in class etomica.integrator.IntegratorGear4NPH.EnsembleToggler
setBoolean(boolean) - Method in interface etomica.modifier.ModifierBoolean: Sets the modified value to the given boolean.
setBoolean(boolean) - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
setBorderAlignment(int) - Method in class etomica.graphics.DeviceSlider
setBorderAlignment(int) - Method in class etomica.graphics.DeviceSpinner
setBorderBackground(Color) - Method in class etomica.graphics.DeviceBox
setBoundaries(int, double[], int[]) - Method in class etomica.modules.rosmosis.MeterFlux
setBoundary(IBoundary) - Method in interface etomica.api.IBox: Sets the box's boundary to the given IBoundary.
setBoundary(IBoundary) - Method in class etomica.box.Box
setBoundaryFrameColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Sets the color of the box boundary.
setBoundaryFrameColor(Color) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Sets the color of the box boundary.
setBoundaryPadding(double) - Method in class etomica.config.ConfigurationLattice
setBoundaryVectors(double[]) - Method in class g3dsys.control.G3DSys: Sets the boundary vectors to be used for calculating image shells
setBoundaryVectors(double[]) - Method in class g3dsys.images.ImageShell
setBoundaryVectorsIterator(IndexIterator) - Method in class g3dsys.control.G3DSys: Sets the index iterator to use for calculating image shells
setBoundaryVectorsIterator(IndexIterator) - Method in class g3dsys.images.ImageShell
setBoundaryWall(boolean) - Method in class etomica.nbr.CriterionPositionWall: Sets whether the walls are at the box boundaries or not.
setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.util.BoxInfo
setBoundingBox(IVector, IVector) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Sets the display bounding box.
setBoundingBox(float, float, float, float, float, float) - Method in class g3dsys.control.G3DSys: Set the min and maximum coordinates for the model.
setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvas1D
setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvas2D
setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytope
setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
setBounds(int, int, int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
setBox(IBox) - Method in interface etomica.action.BoxAction
setBox(IBox) - Method in class etomica.action.BoxActionAdapter
setBox(IBox) - Method in class etomica.action.BoxQuench
setBox(IBox) - Method in class etomica.action.PDBWriter
setBox(IBox) - Method in class etomica.action.WriteConfiguration: Sets the box whose atom coordinates get written to the file.
setBox(IBox) - Method in class etomica.action.WriteConfigurationBinary: Sets the box whose atom coordinates get written to the file.
setBox(IBox) - Method in class etomica.action.WriteConfigurationDLPOLY: Sets the box whose atom coordinates get written to the file.
setBox(IBox) - Method in class etomica.action.WriteConfigurationP2DLPOLY: Sets the box whose atom coordinates get written to the file.
setBox(IBox) - Method in interface etomica.api.IBoundary: Sets the box that holds the IBoundary.
setBox(IBox) - Method in interface etomica.api.IPotential: Informs the potential of the box on which it acts so that it can properly consider the boundaries.
setBox(IBox) - Method in class etomica.association.AtomSourceRandomDimer
setBox(IBox) - Method in class etomica.association.AtomSourceRandomSmer
setBox(IBox) - Method in class etomica.association.BiasVolume2SiteAceticAcid
setBox(IBox) - Method in class etomica.association.BiasVolumeAceticAcid
setBox(IBox) - Method in class etomica.association.BiasVolumeCube
setBox(IBox) - Method in class etomica.association.BiasVolumeSphere
setBox(IBox) - Method in class etomica.association.BiasVolumeSphereOriented
setBox(IBox) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
setBox(IBox) - Method in class etomica.association.MCMoveBiasUB
setBox(IBox) - Method in class etomica.association.MCMoveBiasUBMolecule
setBox(IBox) - Method in class etomica.association.MCMoveDimer
setBox(IBox) - Method in class etomica.association.MCMoveDimerRotate
setBox(IBox) - Method in class etomica.association.MCMoveSmer
setBox(IBox) - Method in class etomica.association.MCMoveSmerRotate
setBox(IBox) - Method in class etomica.association.MCMoveVolumeAssociated
setBox(IBox) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
setBox(IBox) - Method in class etomica.association.MeterDimerMoleFraction
setBox(IBox) - Method in class etomica.association.MoleculeSourceRandomDimer
setBox(IBox) - Method in interface etomica.atom.AtomSource: sets the Box the source should pull Atoms from.
setBox(IBox) - Method in class etomica.atom.AtomSourceRandomLeaf
setBox(IBox) - Method in class etomica.atom.AtomSourceRandomSpecies
setBox(IBox) - Method in class etomica.atom.iterator.ApiLeafAtoms: Conditions iterator to return all leaf-atom pairs from the given box.
setBox(IBox) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType: Sets the box containing the molecules for iteration.
setBox(IBox) - Method in class etomica.atom.iterator.AtomIteratorLeafAtoms: Configures iterator to form its iterates from the leaf atoms of the given box.
setBox(IBox) - Method in interface etomica.atom.iterator.AtomsetIteratorBoxDependent: Sets the Box to pull iterates from
setBox(IBox) - Method in class etomica.atom.iterator.MoleculeIteratorAll: Sets the box containing the molecules for iteration.
setBox(IBox) - Method in class etomica.atom.iterator.MoleculeIteratorAllMolecules: Sets the box having the molecules to be returned as iterates.
setBox(IBox) - Method in class etomica.atom.iterator.MoleculeIteratorMolecule: Sets the box containing the molecules for iteration.
setBox(IBox) - Method in interface etomica.atom.iterator.MoleculesetIteratorBoxDependent: Sets the Box to pull iterates from
setBox(IBox) - Method in class etomica.atom.iterator.MpiInterspecies1A: Configures iterator to return molecules from the set species in the given box.
setBox(IBox) - Method in class etomica.atom.iterator.MpiInterspeciesAA: Configures iterator to return molecules from the set species in the given box.
setBox(IBox) - Method in class etomica.atom.iterator.MpiIntraspecies1A: Configures iterator to return molecules from the set species in the given box.
setBox(IBox) - Method in class etomica.atom.iterator.MpiIntraspeciesAA: Configures iterator to return molecules from the set species in the given box.
setBox(IBox) - Method in class etomica.atom.iterator.MpiMolecule: Specifies the box from which iterates are taken.
setBox(IBox) - Method in interface etomica.atom.MoleculeSource: sets the Box the source should pull Atoms from.
setBox(IBox) - Method in class etomica.atom.MoleculeSourceRandomMolecule
setBox(IBox) - Method in class etomica.atom.MoleculeToMoleculeListSpecies
setBox(IBox) - Method in interface etomica.box.RandomPositionSource: Notifies the RandomPositionSource of the box from which random positions should be taken from.
setBox(IBox) - Method in class etomica.box.RandomPositionSourceDeformable
setBox(IBox) - Method in class etomica.box.RandomPositionSourceRectangular
setBox(IBox) - Method in class etomica.data.DataProcessorInterfacialTension
setBox(IBox) - Method in interface etomica.data.DataSourcePositioned
setBox(IBox) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
setBox(IBox) - Method in class etomica.data.meter.MeterAvgBondLength
setBox(IBox) - Method in class etomica.data.meter.MeterBondOrderParameterQ
setBox(IBox) - Method in class etomica.data.meter.MeterDensity
setBox(IBox) - Method in class etomica.data.meter.MeterDihedralAngle
setBox(IBox) - Method in class etomica.data.meter.MeterDipoleSumSquared1site
setBox(IBox) - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
setBox(IBox) - Method in class etomica.data.meter.MeterHyperVirial
setBox(IBox) - Method in class etomica.data.meter.MeterKineticEnergy
setBox(IBox) - Method in class etomica.data.meter.MeterKineticEnergyRigid: Sets the box to the given box.
setBox(IBox) - Method in class etomica.data.meter.MeterMoleFraction
setBox(IBox) - Method in class etomica.data.meter.MeterMomentumCOM
setBox(IBox) - Method in class etomica.data.meter.MeterNMolecules
setBox(IBox) - Method in class etomica.data.meter.MeterPositionCOM
setBox(IBox) - Method in class etomica.data.meter.MeterPotentialEnergy
setBox(IBox) - Method in class etomica.data.meter.MeterPressure
setBox(IBox) - Method in class etomica.data.meter.MeterPressureTensor: Sets the integrator associated with this instance.
setBox(IBox) - Method in class etomica.data.meter.MeterProfile
setBox(IBox) - Method in class etomica.data.meter.MeterProfileByAtoms
setBox(IBox) - Method in class etomica.data.meter.MeterProfileByVolume
setBox(IBox) - Method in class etomica.data.meter.MeterRadiusGyration
setBox(IBox) - Method in class etomica.data.meter.MeterRDF
setBox(IBox) - Method in class etomica.data.meter.MeterRDFPC
setBox(IBox) - Method in class etomica.data.meter.MeterTensorVelocity
setBox(IBox) - Method in class etomica.data.meter.MeterVolume
setBox(IBox) - Method in class etomica.data.meter.MeterWidomInsertion
setBox(IBox) - Method in class etomica.data.meter.PotentialCalculationRDF
setBox(IBox) - Method in class etomica.freeenergy.npath.DataSourceEnergies
setBox(IBox) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
setBox(IBox) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
setBox(IBox) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
setBox(IBox) - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
setBox(IBox) - Method in class etomica.graphics.DeviceNSelector
setBox(IBox) - Method in class etomica.graphics.DisplayBox: Specifies the box for this display.
setBox(IBox) - Method in class etomica.integrator.IntegratorBox: Performs activities needed to set up integrator to work on given box.
setBox(IBox) - Method in class etomica.integrator.IntegratorConNVT
setBox(IBox) - Method in class etomica.integrator.IntegratorGear4
setBox(IBox) - Method in class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
setBox(IBox) - Method in class etomica.integrator.IntegratorGear4NPH
setBox(IBox) - Method in class etomica.integrator.IntegratorHard
setBox(IBox) - Method in class etomica.integrator.IntegratorMC: Invokes superclass method and informs all MCMoves about the new box.
setBox(IBox) - Method in class etomica.integrator.IntegratorMD
setBox(IBox) - Method in class etomica.integrator.IntegratorRigidIterative
setBox(IBox) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
setBox(IBox) - Method in class etomica.integrator.IntegratorVelocityVerlet
setBox(IBox) - Method in class etomica.integrator.IntegratorVelocityVerletShake
setBox(IBox) - Method in class etomica.integrator.IntegratorVerlet
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveAtom
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveBox: Sets the box on which this move acts.
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveBoxSize
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveDimer
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveManager: Invokes superclass method and informs all MCMoves about the new box.
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveMolecule
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveRotate
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveSemigrand: Extends the superclass method to initialize the exchange-set species agents for the box.
setBox(IBox) - Method in class etomica.integrator.mcmove.MCMoveVolume
setBox(IBox) - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
setBox(IBox) - Method in class etomica.liquidLJ.MeterPU
setBox(IBox) - Method in class etomica.liquidLJ.MeterPUCut
setBox(IBox) - Method in class etomica.liquidLJ.MeterPUCutLS
setBox(IBox) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
setBox(IBox) - Method in class etomica.liquidLJ.MeterWidomInsertionP
setBox(IBox) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
setBox(IBox) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
setBox(IBox) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
setBox(IBox) - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
setBox(IBox) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
setBox(IBox) - Method in class etomica.meam.PotentialCuLREP
setBox(IBox) - Method in class etomica.meam.PotentialEFS
setBox(IBox) - Method in class etomica.meam.PotentialFeEAM
setBox(IBox) - Method in class etomica.meam.PotentialFeEAM_LS
setBox(IBox) - Method in class etomica.meam.PotentialMEAM
setBox(IBox) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
setBox(IBox) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
setBox(IBox) - Method in class etomica.models.co2.P2CO2H2OWheatley
setBox(IBox) - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
setBox(IBox) - Method in class etomica.models.co2.P2CO2Hellmann
setBox(IBox) - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
setBox(IBox) - Method in class etomica.models.co2.PNCO2GCPM
setBox(IBox) - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
setBox(IBox) - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
setBox(IBox) - Method in class etomica.models.co2.PNGCPM
setBox(IBox) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
setBox(IBox) - Method in class etomica.models.hexane.MCMoveCBMC
setBox(IBox) - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
setBox(IBox) - Method in class etomica.models.hexane.MCMoveReptate
setBox(IBox) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
setBox(IBox) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
setBox(IBox) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
setBox(IBox) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
setBox(IBox) - Method in class etomica.models.nitrogen.P2Nitrogen
setBox(IBox) - Method in class etomica.models.nitrogen.P2NitrogenAB
setBox(IBox) - Method in class etomica.models.nitrogen.P2NitrogenAnisotropic
setBox(IBox) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
setBox(IBox) - Method in class etomica.models.nitrogen.PRotConstraint
setBox(IBox) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setBox(IBox) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
setBox(IBox) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
setBox(IBox) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
setBox(IBox) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
setBox(IBox) - Method in class etomica.models.water.P2Water3P
setBox(IBox) - Method in class etomica.models.water.P2Water4P
setBox(IBox) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
setBox(IBox) - Method in class etomica.models.water.P2WaterSzalewicz
setBox(IBox) - Method in class etomica.models.water.P2WaterTIP4PHardCore
setBox(IBox) - Method in class etomica.models.water.PNWaterGCPM
setBox(IBox) - Method in class etomica.modules.adsorption.IntegratorHybrid
setBox(IBox) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
setBox(IBox) - Method in class etomica.modules.adsorption.MyMCMove
setBox(IBox) - Method in class etomica.modules.adsorption.P1Wall
setBox(IBox) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
setBox(IBox) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
setBox(IBox) - Method in class etomica.modules.chainequilibrium.MeterChainLength
setBox(IBox) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
setBox(IBox) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
setBox(IBox) - Method in class etomica.modules.colloid.MeterEnd2End
setBox(IBox) - Method in class etomica.modules.colloid.P1Wall
setBox(IBox) - Method in class etomica.modules.dcvgcmd.MeterFlux
setBox(IBox) - Method in class etomica.modules.dcvgcmd.MyMCMove
setBox(IBox) - Method in class etomica.modules.droplet.IntegratorDroplet
setBox(IBox) - Method in class etomica.modules.droplet.MeterDeformation
setBox(IBox) - Method in class etomica.modules.droplet.P1Smash
setBox(IBox) - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
setBox(IBox) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
setBox(IBox) - Method in class etomica.modules.entropylottery.MeterEntropy
setBox(IBox) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
setBox(IBox) - Method in class etomica.modules.interfacial.MeterOrientation
setBox(IBox) - Method in class etomica.modules.materialfracture.MeterElongation
setBox(IBox) - Method in class etomica.modules.materialfracture.MeterStrain
setBox(IBox) - Method in class etomica.modules.materialfracture.MeterStress
setBox(IBox) - Method in class etomica.modules.materialfracture.P1Tension
setBox(IBox) - Method in class etomica.modules.materialfracture.StrainColorScheme
setBox(IBox) - Method in class etomica.modules.mu.P1MagicWall
setBox(IBox) - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
setBox(IBox) - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
setBox(IBox) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
setBox(IBox) - Method in class etomica.modules.render.RenderMD.CriterionCar
setBox(IBox) - Method in class etomica.modules.rheology.MeterEndToEnd
setBox(IBox) - Method in class etomica.modules.rheology.MeterNormalStress
setBox(IBox) - Method in class etomica.modules.rheology.MeterViscosity
setBox(IBox) - Method in class etomica.modules.rosmosis.MeterFlux
setBox(IBox) - Method in class etomica.modules.sam.CriterionTether3
setBox(IBox) - Method in class etomica.modules.sam.MeterTilt
setBox(IBox) - Method in class etomica.modules.sam.MeterWallPressure
setBox(IBox) - Method in class etomica.modules.sam.P1Sinusoidal
setBox(IBox) - Method in class etomica.modules.vle.MeterPressure2
setBox(IBox) - Method in class etomica.nbr.cell.Api1ACell
setBox(IBox) - Method in class etomica.nbr.cell.AtomIteratorCell
setBox(IBox) - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
setBox(IBox) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
setBox(IBox) - Method in class etomica.nbr.CriterionAdapter: Specifies to the wrapped criterion the box where the criterion is being applied.
setBox(IBox) - Method in class etomica.nbr.CriterionAll: Performs no action.
setBox(IBox) - Method in class etomica.nbr.CriterionNone: Performs no action.
setBox(IBox) - Method in class etomica.nbr.CriterionPositionWall
setBox(IBox) - Method in class etomica.nbr.CriterionSimple
setBox(IBox) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular: Specifies to the wrapped criterion the box where the criterion is being applied.
setBox(IBox) - Method in class etomica.nbr.molecule.CriterionAllMolecular: Performs no action.
setBox(IBox) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
setBox(IBox) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular: Specifies the box where the criterion is being applied.
setBox(IBox) - Method in interface etomica.nbr.NeighborCriterion: Specifies the box where the criterion is being applied.
setBox(IBox) - Method in class etomica.nbr.site.Api1ASite
setBox(IBox) - Method in class etomica.normalmode.DeviceCellNum3DSlider
setBox(IBox) - Method in class etomica.normalmode.DeviceCellNumXYSlider
setBox(IBox) - Method in class etomica.normalmode.IntegratorHardMDMC
setBox(IBox) - Method in class etomica.normalmode.IntegratorHarmonic
setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomCoupled
setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
setBox(IBox) - Method in class etomica.normalmode.MCMoveAtomSuperBox
setBox(IBox) - Method in class etomica.normalmode.MCMoveHarmonic
setBox(IBox) - Method in class etomica.normalmode.MCMoveHarmonicStep
setBox(IBox) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
setBox(IBox) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
setBox(IBox) - Method in class etomica.normalmode.MCMoveSingleMode
setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeSolid
setBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
setBox(IBox) - Method in class etomica.normalmode.MCMoveWV
setBox(IBox) - Method in class etomica.normalmode.MeterAPIPotentialEnergy
setBox(IBox) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
setBox(IBox) - Method in class etomica.normalmode.MeterNormalMode: Sets the box, and should be called while the Atoms are in their lattice positions.
setBox(IBox) - Method in class etomica.normalmode.MeterOverlapSwitch
setBox(IBox) - Method in class etomica.normalmode.MeterPhiDeviation
setBox(IBox) - Method in class etomica.normalmode.MeterPlaneSlip
setBox(IBox) - Method in class etomica.normalmode.MeterThetaDeviation
setBox(IBox) - Method in class etomica.normalmode.MeterTilt
setBox(IBox) - Method in class etomica.normalmode.MeterTiltHistogram
setBox(IBox) - Method in class etomica.normalmode.MeterTiltRotation
setBox(IBox) - Method in class etomica.normalmode.MeterTiltRotationHistogram
setBox(IBox) - Method in class etomica.normalmode.MeterTiltRotationStdev
setBox(IBox) - Method in class etomica.normalmode.P1ConstraintNbr
setBox(IBox) - Method in class etomica.normalmode.P1ConstraintNbrHcp
setBox(IBox) - Method in class etomica.normalmode.P2XOrder
setBox(IBox) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
setBox(IBox) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
setBox(IBox) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
setBox(IBox) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
setBox(IBox) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setBox(IBox) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setBox(IBox) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
setBox(IBox) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
setBox(IBox) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
setBox(IBox) - Method in class etomica.potential.EwaldSummation
setBox(IBox) - Method in class etomica.potential.EwaldSumMolecules
setBox(IBox) - Method in class etomica.potential.P1ExternalField
setBox(IBox) - Method in class etomica.potential.P1HardBoundary
setBox(IBox) - Method in class etomica.potential.P1HarmonicSite
setBox(IBox) - Method in class etomica.potential.P1HydrogenMielke
setBox(IBox) - Method in class etomica.potential.P22CLJQ
setBox(IBox) - Method in class etomica.potential.P2CO2EMP
setBox(IBox) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
setBox(IBox) - Method in class etomica.potential.P2DLPOLY
setBox(IBox) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
setBox(IBox) - Method in class etomica.potential.P2HardAssociationCone
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeFourSites
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeOneSite
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeReference
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
setBox(IBox) - Method in class etomica.potential.P2HardAssociationConeSW
setBox(IBox) - Method in class etomica.potential.P2HardBondedList
setBox(IBox) - Method in class etomica.potential.P2HardWrapper
setBox(IBox) - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
setBox(IBox) - Method in class etomica.potential.P2HePCKLJS.P2HeTI
setBox(IBox) - Method in class etomica.potential.P2HeSimplified.P2HeQFH
setBox(IBox) - Method in class etomica.potential.P2HeSimplified.P2HeTI
setBox(IBox) - Method in class etomica.potential.P2HSDipole
setBox(IBox) - Method in class etomica.potential.P2HydrogenHinde
setBox(IBox) - Method in class etomica.potential.P2HydrogenHindeAtomic
setBox(IBox) - Method in class etomica.potential.P2HydrogenHindePatkowski
setBox(IBox) - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
setBox(IBox) - Method in class etomica.potential.P2HydrogenPatkowski
setBox(IBox) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
setBox(IBox) - Method in class etomica.potential.P2Ideal: Does nothing.
setBox(IBox) - Method in class etomica.potential.P2LJDipole
setBox(IBox) - Method in class etomica.potential.P2LJQ
setBox(IBox) - Method in class etomica.potential.P2LJQQ
setBox(IBox) - Method in class etomica.potential.P2MoleculeMonatomic
setBox(IBox) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
setBox(IBox) - Method in class etomica.potential.P2MoleculeTruncated
setBox(IBox) - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
setBox(IBox) - Method in class etomica.potential.P2NitrogenHellmann
setBox(IBox) - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
setBox(IBox) - Method in class etomica.potential.P2O2Bartolomei
setBox(IBox) - Method in class etomica.potential.P2QChem
setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipole
setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
setBox(IBox) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
setBox(IBox) - Method in class etomica.potential.P2SemiclassicalAtomic
setBox(IBox) - Method in class etomica.potential.P2SemiclassicalMolecular
setBox(IBox) - Method in class etomica.potential.P2SoftSphericalTruncated
setBox(IBox) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
setBox(IBox) - Method in class etomica.potential.P2SoftTruncated
setBox(IBox) - Method in class etomica.potential.P2SpheroPolyhedron
setBox(IBox) - Method in class etomica.potential.P2SquareWellRobust
setBox(IBox) - Method in class etomica.potential.P2TriangleWell
setBox(IBox) - Method in class etomica.potential.P2WaterPotentialsJankowski
setBox(IBox) - Method in class etomica.potential.P3AxilrodTeller
setBox(IBox) - Method in class etomica.potential.P3BondAngle
setBox(IBox) - Method in class etomica.potential.P3BondAngleDreiding
setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHe
setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setBox(IBox) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
setBox(IBox) - Method in class etomica.potential.P3HydrogenATM
setBox(IBox) - Method in class etomica.potential.P3HydrogenManzhos
setBox(IBox) - Method in class etomica.potential.P3Induction
setBox(IBox) - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
setBox(IBox) - Method in class etomica.potential.P4BondTorsion
setBox(IBox) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
setBox(IBox) - Method in class etomica.potential.P4TorsionDreiding
setBox(IBox) - Method in class etomica.potential.Potential: Informs the potential of the box on which it acts.
setBox(IBox) - Method in class etomica.potential.Potential0Lrc
setBox(IBox) - Method in class etomica.potential.Potential1
setBox(IBox) - Method in class etomica.potential.Potential2HardSpherical
setBox(IBox) - Method in class etomica.potential.Potential2SoftSpherical
setBox(IBox) - Method in class etomica.potential.Potential2SoftSphericalLS
setBox(IBox) - Method in class etomica.potential.PotentialAtomicSum
setBox(IBox) - Method in class etomica.potential.PotentialCalculationPressureTensor
setBox(IBox) - Method in class etomica.potential.PotentialDLPOLY
setBox(IBox) - Method in class etomica.potential.PotentialEmul
setBox(IBox) - Method in class etomica.potential.PotentialGroup
setBox(IBox) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
setBox(IBox) - Method in class etomica.potential.PotentialMolecular: Informs the potential of the box on which it acts.
setBox(IBox) - Method in class etomica.potential.PotentialMolecularMonatomic
setBox(IBox) - Method in class etomica.potential.PotentialMolecularSum
setBox(Box) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
setBox(IBox) - Method in class etomica.rotation.P2LJDipole
setBox(IBox) - Method in class etomica.space.Boundary: Sets the boundary's box to be the given box.
setBox(IBox) - Method in class etomica.spin.MCMoveSpinFlip
setBox(IBox) - Method in class etomica.spin.MeterSpin
setBox(IBox) - Method in class etomica.spin.P2Spin
setBox(IBox) - Method in class etomica.threaded.PotentialThreaded
setBox(IBox) - Method in class etomica.virial.ClusterSumIC.FR2
setBox(BoxCluster) - Method in interface etomica.virial.ClusterWeightSumWall.DataSourceClusterWall
setBox(IBox) - Method in class etomica.virial.MayerD2FDT2Spherical
setBox(IBox) - Method in class etomica.virial.MayerDFDTSpherical
setBox(IBox) - Method in class etomica.virial.MayerDFQFHDTSpherical
setBox(IBox) - Method in class etomica.virial.MayerEGeneral
setBox(IBox) - Method in class etomica.virial.MayerEHardSphere
setBox(IBox) - Method in class etomica.virial.MayerENonGeneral
setBox(IBox) - Method in class etomica.virial.MayerESpherical
setBox(IBox) - Method in interface etomica.virial.MayerFunction
setBox(IBox) - Method in class etomica.virial.MayerFunctionMolecularThreeBody
setBox(IBox) - Method in interface etomica.virial.MayerFunctionNonAdditive
setBox(IBox) - Method in class etomica.virial.MayerFunctionNonAdditiveFull
setBox(IBox) - Method in class etomica.virial.MayerFunctionProductGeneral
setBox(IBox) - Method in class etomica.virial.MayerFunctionSphericalThreeBody
setBox(IBox) - Method in class etomica.virial.MayerFunctionSum
setBox(IBox) - Method in class etomica.virial.MayerFunctionSumGeneral
setBox(IBox) - Method in class etomica.virial.MayerFunctionTemperature
setBox(IBox) - Method in class etomica.virial.MayerFunctionThreeBody
setBox(IBox) - Method in class etomica.virial.MayerGeneral
setBox(IBox) - Method in class etomica.virial.MayerGeneralAtomic
setBox(IBox) - Method in class etomica.virial.MayerGeneralSpherical
setBox(IBox) - Method in class etomica.virial.MayerHardSphere
setBox(IBox) - Method in class etomica.virial.MayerPTAtt
setBox(IBox) - Method in class etomica.virial.MayerPUGeneral
setBox(IBox) - Method in class etomica.virial.MayerSphericalPlus
setBox(IBox) - Method in class etomica.virial.MayerSphericalPTAtt
setBox(IBox) - Method in class etomica.virial.MayerSSSeries
setBox(IBox) - Method in class etomica.virial.MayerWell
setBox(IBox) - Method in class etomica.virial.MayerXSpherical
setBox(IBox) - Method in class etomica.virial.MCMoveChangeBondLength
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAngleBend
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtom
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomHSRing
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomHSTree
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomMulti
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomQ
setBox(IBox) - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
setBox(IBox) - Method in class etomica.virial.MCMoveClusterDiagram
setBox(IBox) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
setBox(IBox) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
setBox(IBox) - Method in class etomica.virial.MCMoveClusterReptateMulti
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingRegrow
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRingScale
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRotateCH3
setBox(IBox) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
setBox(IBox) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
setBox(IBox) - Method in class etomica.virial.MCMoveClusterTorsionMulti
setBox(IBox) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
setBox(IBox) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
setBox(IBox) - Method in class etomica.virial.MCMoveClusterWiggleMulti
setBox(BoxCluster) - Method in class etomica.virial.MeterSamplingWeight
setBox(BoxCluster) - Method in class etomica.virial.MeterVirial
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBD
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBDBin
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBinMultiThreaded
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalField
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldConfined
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldRho
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldSW
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialIC
setBox(BoxCluster) - Method in class etomica.virial.MeterVirialSWWE
setBox(IBox) - Method in class etomica.virial.MuFGeneral
setBox(IBox) - Method in class etomica.virial.MuGeneral
setBox(IBox) - Method in class etomica.virial.P1IntraLambda
setBox(IBox) - Method in class etomica.virial.PotentialCommonAtomic
setBox(IBox) - Method in class etomica.virial.PotentialEmulCached
setBox(IBox) - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
setBox(IBox) - Method in class etomica.virial.PotentialGroup3PI
setBox(IBox) - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
setBox(IBox) - Method in class etomica.virial.PotentialGroupPI
setBox(IBox) - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
setBox(IBox) - Method in class etomica.virial.PotentialNonAdditive
setBox(IBox) - Method in class etomica.yukawa.P2HC2Yukawa
setBox(IBox) - Method in class etomica.zeolite.MSDCoordWriter
setBoxCanvas(DisplayCanvas) - Method in class etomica.graphics.DisplayBox
setBoxFactory(SimulationVirialOverlap2.BoxClusterFactory) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setBoxIndex(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
setBoxSize(IVector) - Method in interface etomica.api.IBoundary: Scales the boundary dimensions such that the boundary's would be inscribed within a rectangle of the of the given size.
setBoxSize(IBox, int[]) - Method in class etomica.config.GrainBoundaryTiltConfiguration: Resizes simulation box to preserve periodic boundary conditions after rotation of lattice.
setBoxSize(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic: Scales each boundary edge so that its length equals the corresponding value in the given vector.
setBoxSize(IVector) - Method in class etomica.space.BoundaryRectangular: Sets the size and shape of the rectangular boundary.
setBoxSize(IVector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
setBPRes(double[]) - Method in class etomica.normalmode.MeterSolidDACut
setBXX(double) - Method in class etomica.models.rowley.P2RepRowley
setC(double, double) - Method in class etomica.normalmode.MinimizeHCP
setC(double) - Method in class etomica.potential.P2Exp6
setCaching(boolean) - Method in class etomica.virial.ClusterSum
setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizable
setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
setCapacity(int) - Method in class etomica.nbr.list.AtomNeighborLists: Sets the number of up and down lists maintained by this instance.
setCapacity(int) - Method in class etomica.nbr.list.AtomPotentialList
setCapacity(int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists: Sets the number of up and down lists maintained by this instance.
setCapacity(int) - Method in class etomica.nbr.list.molecule.MoleculePotentialList
setCellDensity(double) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
setCellDensity(double) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
setCellDensity(double) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
setCellRange(int) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Sets the cell range to the given value.
setCellRange(int) - Method in class etomica.nbr.cell.NeighborCellManager: Sets the cell range to the given value.
setCellRange(int) - Method in class etomica.nbr.cell.PotentialMasterCell
setCellRange(int) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
setCellRange(int) - Method in class etomica.nbr.list.PotentialMasterList
setCellRange(int) - Method in class etomica.nbr.PotentialMasterHybrid
setCellRange(int) - Method in class etomica.nbr.site.PotentialMasterSite
setCellSize(double, double) - Method in class etomica.modules.sam.P1Sinusoidal
setCellSizeX(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setCellSizeX(double) - Method in class etomica.modules.sam.ConfigurationSAM
setCellSizeZ(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setCellSizeZ(double) - Method in class etomica.modules.sam.ConfigurationSAM
setCenterOfRotation(Point3f) - Method in class g3dsys.control.G3DSys: Set the molecule space location around which rotation occurs
setCH2element(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
setCH3element(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
setChainlength(int) - Method in class etomica.models.hexane.MCMoveCBMC
setChainLength(int) - Method in class etomica.modules.colloid.ColloidSim
setChainLength(int) - Method in class etomica.modules.colloid.ConfigurationColloid
setChainLength(int) - Method in class etomica.modules.colloid.MeterEnd2End
setChainLength(int) - Method in class etomica.modules.colloid.NeighborListManagerColloid
setChainLength(int) - Method in class etomica.modules.rheology.SimulationRheology
setChainLength(int) - Method in class etomica.modules.sam.Sam
setChainPhi(int, double) - Method in class etomica.modules.sam.Sam
setChainPsi(double) - Method in class etomica.modules.sam.Sam
setChainTheta(double) - Method in class etomica.modules.sam.Sam
setChangeableModes(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV: Set the wavevectors that can be changed by the move.
setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
setCharge1(double) - Method in class etomica.potential.P2Electrostatic: Sets the charge on the first type of atom.
setCharge1(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore: Sets the charge on the first type of atom.
setCharge2(double) - Method in class etomica.potential.P2Electrostatic: Sets the charge on the second type of atom.
setCharge2(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore: Sets the charge on the second type of atom.
setChildCount(int[]) - Method in class etomica.species.SpeciesSpheresHetero: Directly sets the number of child atoms of each type created by this factory.
setChildIndex(int) - Method in interface etomica.api.IAtomType
setChildIndex(int) - Method in class etomica.atom.AtomTypeLeaf
setChildTypes(IAtomType[]) - Method in class etomica.species.SpeciesSpheresCustom: Sets the factories that make the child atoms of this factory's atom.
setChildTypes(IAtomType[]) - Method in class etomica.species.SpeciesSpheresHetero: Sets the factories that make the child atoms of this factory's atom.
setClient(Object) - Method in class etomica.simulation.DataStreamHeader
setCloseFileEachTime(boolean) - Method in class etomica.data.DataLogger: Close the file and open a new one at each time INTERVAL.
setCloseWindow(JButton) - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
setCloseWindow(JButton) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
setColix(short) - Method in class org.jmol.g3d.Graphics3D: sets current color from colix color index
setColix(short) - Method in class org.jmol.util.GData
setColix(short) - Method in class org.jmol.util.MeshSurface
setColixBack(short) - Method in class org.jmol.util.MeshSurface
setCollapseOnReset(boolean) - Method in class etomica.util.HistoryComplete: Sets a flag that determines if the history is collapsed (to 100 data points) when reset is called.
setCollision(double, IAtom, PotentialHard) - Method in class etomica.integrator.IntegratorHard.Agent: Sets parameters associated with next two-body collision of this atom with another atom.
setCollisionDiameter(double) - Method in class etomica.potential.P2HardSphere: Accessor method for collision diameter
setCollisionRadius(double) - Method in class etomica.modules.osmosis.MeterOsmoticPressure: Sets the collision radius used to calculate accessible "area" assuming that the relevant hard "boundaries" form right-angles with other hard boundaries.
setCollisionRadius(double) - Method in class etomica.modules.osmosis.P1HardWall: Distance from the center of the sphere to the boundary at collision.
setCollisionRadius(double) - Method in class etomica.potential.P1HardBoundary: Distance from the center of the sphere to the boundary at collision.
setCollisionRadius(double) - Method in class etomica.potential.P1HardMovingBoundary: Distance from the center of the sphere to the boundary at collision.
setColloidMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
setColloidSigma(double) - Method in class etomica.modules.colloid.ColloidSim
setColor(char) - Method in interface etomica.graph.model.Edge
setColor(char) - Method in class etomica.graph.model.impl.EdgeImpl
setColor(char) - Method in class etomica.graph.model.impl.NodeImpl
setColor(char) - Method in interface etomica.graph.model.Node
setColor(IAtomType, Color) - Method in class etomica.graphics.ColorSchemeByType
setColor(IAtomType, int, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise: Sets atoms of the given type and number of bonds to be the given color.
setColor(String) - Method in class etomica.modules.clustergenerator.Plot
setColor(short) - Method in class g3dsys.images.Axes: set the color of the figure
setColor(short) - Method in class g3dsys.images.Ball: set the color of the figure
setColor(short) - Method in class g3dsys.images.Box: set the color of the figure
setColor(short) - Method in class g3dsys.images.Ellipse: set the color of the figure
setColor(short) - Method in class g3dsys.images.Line: set the color of the figure
setColor(short) - Method in class g3dsys.images.Triangle: set the color of the figure
setColor(int) - Method in class org.jmol.g3d.Graphics3D
setColor(int) - Method in class org.jmol.util.GData
setColorIn(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane: Color for atoms that are in the plane.
setColorOut(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane: Color for atoms that are out of the plane.
setColorScheme(ColorScheme) - Method in class etomica.graphics.DisplayBox: Mutator method for the color scheme used for this display
setColumn(int, float, float, float) - Method in class org.jmol.util.Matrix3f: Sets the specified column of this matrix3d to the three values provided.
setColumn(int, float[]) - Method in class org.jmol.util.Matrix4f: Sets the specified column of this matrix4f to the four values provided.
setColumn4(int, float, float, float, float) - Method in class org.jmol.util.Matrix4f: Sets the specified column of this matrix4f to the four values provided.
setColumnA(int, float[]) - Method in class org.jmol.util.Matrix3f: Sets the specified column of this matrix3d to the four values provided.
setColumnHeader(DataTag[], String) - Method in class etomica.graphics.DisplayTable
setColumnInfoFactories(DataDoubleArray.DataInfoDoubleArrayFactory[]) - Method in class etomica.data.types.DataTable.DataInfoTableFactory: Sets the DataInfoFactories for the columns
setColumnNames(String[]) - Method in class etomica.graphics.DeviceTableModelGeneric
setColumnV(int, Vector3f) - Method in class org.jmol.util.Matrix3f: Sets the specified column of this matrix3d to the vector provided.
setCombinationProbability(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical: Sets the probability that two radicals will bond instead of becoming unreactive.
setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV: Set the wavevectors that are removed.
setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setComparedWV(int) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
setComponent(Object) - Method in class etomica.graphics.DeviceSlider
setComponent(Object) - Method in class etomica.graphics.DeviceSpinner
setComponent(PNCO2GCPM.Component) - Method in class etomica.models.co2.PNCO2GCPM
setComponent(PNGCPM.Component) - Method in class etomica.models.co2.PNGCPM
setComponent(P2WaterSzalewicz.Component) - Method in class etomica.models.water.P2WaterSzalewicz
setComponent(int, int, double) - Method in interface etomica.space.Tensor
setComponent(int, int, double) - Method in class etomica.space1d.Tensor1D
setComponent(int, int, double) - Method in class etomica.space2d.Tensor2D
setComponent(int, int, double) - Method in class etomica.space3d.Tensor3D
setComponent(int, int, double) - Method in class etomica.spaceNd.TensorND
setComponent(int) - Method in class etomica.util.numerical.CalcGradientDifferentiable
setComponentValues(String[][]) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
setConfigDLPOLY(WriteConfigurationDLPOLY) - Method in class etomica.potential.PotentialDLPOLY
setConfigP2DLPOLY(WriteConfigurationP2DLPOLY) - Method in class etomica.potential.P2DLPOLY
setConfiguration(Configuration) - Method in class etomica.action.SimulationRestart
setConfiguration(Configuration) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setConfiguration(Configuration) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setConfiguration(Configuration) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
setConfiguration(Configuration) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
setConfName(String) - Method in class etomica.action.WriteConfiguration: Sets the configuration name.
setConfName(String) - Method in class etomica.action.WriteConfigurationBinary: Sets the configuration name.
setConfName(String) - Method in class etomica.action.WriteConfigurationDLPOLY: Sets the configuration name.
setConfName(String) - Method in class etomica.action.WriteConfigurationP2DLPOLY: Sets the configuration name.
setConformation(IConformation) - Method in class etomica.chem.models.ModelChain: Sets the Conformation for the molecule.
setConformation(int, ConformationChainZigZag) - Method in class etomica.modules.sam.ConfigurationSAM
setConformation(IConformation) - Method in class etomica.species.Species
setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setConformationParameters(double, double) - Method in class etomica.virial.SpeciesAlkane
setConstrainScriptOrigin(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets whether scripts should only be loaded from the same location as the documents referencing them.
setConstraint(IPotentialAtomic) - Method in class etomica.normalmode.MCMoveAtomCoupled
setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterBoltzmannHTTP
setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterDDP
setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterDP
setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterTargetTP
setConstraintAngle(double) - Method in class etomica.models.nitrogen.MeterDirectInitPert
setConstraintAngle(double) - Method in class etomica.models.nitrogen.PRotConstraint
setConstraintMap(int[]) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
setConstraintMap(int[]) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
setConstructorObject(Integer) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setContainingCubeEdgeLength(double) - Method in class etomica.math.geometry.TruncatedOctahedron: Sets the size of the truncated octahedron in terms of the edge length of a cube that would contain it.
setController(IController) - Method in interface etomica.action.ControllerAction
setController(IController) - Method in class etomica.action.ControllerActionAdapter
setController(IController) - Method in class etomica.graphics.Device
setController(Controller) - Method in class etomica.graphics.DeviceControllerButton
setController(IController) - Method in class etomica.graphics.DeviceThermoSlider: Set the temperature slider controller.
setController(IController) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the temperature slider controller.
setController(IController) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the n- Cell # slider controller.
setController(IController) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the x- and y- Cell # slider controller.
setController(IController) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the eigenvalue # slider controller.
setController(IController) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the wavevector # slider controller.
setConvertedWV(int) - Method in class etomica.models.oneDHardRods.MeterF
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
setCoordinateDefinition(CoordinateDefinitionNitrogen) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.CalcJacobian
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.IntegratorHarmonic
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveHarmonic
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveHarmonicStep
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveSingleMode
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterBoltzmannHTTP
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterDDP
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterDP
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterNormalMode: Sets the object that defines the real-space generalized coordinates.
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterTargetTP
setCoordinateDefinition(CoordinateDefinitionParacetamol) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
setCoordinateDefinitionParacetamol(CoordinateDefinitionParacetamol) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.modules.mu.P2SquareWellOneSide: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.potential.P2DoubleWell: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.potential.P2PenetrableSphere: Mutator method for core diameter.
setCoreDiameter(double) - Method in class etomica.potential.P2PenetrableSquareWell: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.potential.P2SquareWell: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.potential.P2SquareWellRobust: Accessor method for core diameter.
setCoreDiameter(double) - Method in class etomica.potential.P2TriangleWell
setCoreDiameterSquared(double) - Method in class etomica.potential.P2PenetrableSquareWell
setCountOfMoleculesStrings(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setCountOfSpeciesSLM(SpinnerListModel, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setCountOfSpeciesSLMListener(ChangeListener[]) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setCountSpecies(int, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setCoupling(double) - Method in class etomica.spin.P2Spin
setCriterion(IPotentialMolecular, NeighborCriterionMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Sets the criterion associated with the given potential, overriding the default provided by the PotentialMasterList.
setCriterion(IPotentialAtomic, NeighborCriterion) - Method in class etomica.nbr.list.PotentialMasterList: Sets the criterion associated with the given potential, overriding the default provided by the PotentialMasterList.
setCriterion(IPotentialAtomic, NeighborCriterion) - Method in class etomica.nbr.site.PotentialMasterSite: Sets the criterion associated with the given potential, overriding the default provided by the PotentialMasterCell.
setCriterion(IPotential, NeighborCriterion) - Method in class etomica.potential.PotentialArray: Sets the criterion associated with the given potential
setCriterion(IPotentialMolecular, NeighborCriterionMolecular) - Method in class etomica.potential.PotentialArrayMolecular: Sets the criterion associated with the given potential
setCSPotential(P2SquareWellSurface) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveBcc: Sets the length of all primitive vectors to the given value.
setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveFcc: Sets the length of all primitive vectors to the given value.
setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal: Sets the length of all primitive vectors to the given value.
setCursor(int, Object) - Method in interface org.jmol.api.ApiPlatform
setCursor(int, Object) - Method in class org.jmol.awt.Platform
setCutoff(double) - Method in class etomica.modules.droplet.AtomFilterLiquid
setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationCone: Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for Lennard-Jones cutoff distance; divided by sigma
setCutoffRatio(double) - Method in class etomica.potential.P2MoleculeTruncated
setCutoffRatio(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
setCVector(IVectorMutable) - Method in class etomica.action.BoxInflateAnisotropic
setCXX(double) - Method in class etomica.models.rowley.P2RepRowley
setD(float) - Method in class g3dsys.images.Ball: set the molspace diameter of the figure, when applicable
setD(float) - Method in class g3dsys.images.Bond: set the molspace diameter of the figure, when applicable
setD(float) - Method in class g3dsys.images.Ellipse: set the molspace diameter of the figure, when applicable
setD2dfac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother: sets weight given to minimizing discontinuities in the 2nd derivative (at data points)
setD2fac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother: sets weight given to minimizing the 2nd derivative
setD3dfac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother
setD3fac(double) - Method in class etomica.util.numerical.AkimaSplineSmoother: sets weight given to minimizing the 3nd derivative
setDampingParams(int, int, double, int, boolean) - Method in class etomica.potential.P2QChemInterpolated: The energy u.
setData(double[], double[]) - Method in class etomica.util.FastFourierTransform: Saves the two passed arrays of doubles into this class, real and imaginary in order to transform.
setData(double[], boolean) - Method in class etomica.util.FastFourierTransform: For passing only all reals (true) or all imaginaries (false)
setData(double[]) - Method in class etomica.util.FastFourierTransform: For passing only one set of data - assumes passing all reals
setDataResetAction(SimulationDataAction) - Method in class etomica.action.SimulationRestart
setDataSink(int, IDataSink) - Method in class etomica.data.DataDistributer: Sets the DataSink for the ith output stream (corresponding to the ith numerical value coming in).
setDataSink(IDataSink) - Method in class etomica.data.DataFork: Sets the given DataSink as the only one connected to this DataFork.
setDataSink(int, IDataSink) - Method in class etomica.data.DataGroupSplitter: Sets the DataSink for the ith output stream (corresponding to the ith numerical value coming in).
setDataSink(IDataSink) - Method in class etomica.data.DataLogger
setDataSink(IDataSink) - Method in interface etomica.data.DataPipe: Sets the DataSink that will receive data from this DataPipe.
setDataSink(IDataSink) - Method in class etomica.data.DataProcessor: Sets the sink receiving the data.
setDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
setDataSink(int, IDataSink) - Method in class etomica.data.DataSplitter: Sets the DataSink for the ith output stream (corresponding to the ith numerical value coming in).
setDataSinkFactory(DataSplitter.IDataSinkFactory) - Method in class etomica.data.DataSplitter
setDataSinks(IDataSink[]) - Method in class etomica.data.DataFork
setDataSinks(IDataSink[]) - Method in interface etomica.data.DataPipeForked: Sets the list of DataSinks that receive the Data entering this DataFork.
setDataSinks(IDataSink[]) - Method in class etomica.data.DataProcessorForked
setDataSource(DataSourcePositioned) - Method in class etomica.data.meter.MeterProfile: Accessor method for the meter that defines the profiled quantity.
setDataSource(DataSourceMolecular) - Method in class etomica.data.meter.MeterProfileByAtoms: Accessor method for the meter that defines the profiled quantity.
setDataSource(DataSourceMolecular) - Method in class etomica.data.meter.MeterProfileByVolume: Accessor method for the meter that defines the profiled quantity.
setDataSourceA(DataSourceScalar) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
setDataSourceB(DataSourceScalar) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
setDataSourceMuRoot(DataSourceMuRoot) - Method in class etomica.normalmode.DataSourceAvgPressure2
setDecimalMode() - Method in class etomica.util.ScientificFormat
setDecimalSeparatorAlwaysShown(boolean) - Method in class etomica.util.ScientificFormat
setDecimalSliderLabelTable(Hashtable) - Method in class etomica.graphics.DecimalSlider
setDecimalSliderMajorTickSpacing(double) - Method in class etomica.graphics.DecimalSlider
setDecimalSliderMaximum(double) - Method in class etomica.graphics.DecimalSlider
setDecimalSliderMinimum(double) - Method in class etomica.graphics.DecimalSlider
setDecimalSliderMinorTickSpacing(double) - Method in class etomica.graphics.DecimalSlider
setDecimalSliderValue(double) - Method in class etomica.graphics.DecimalSlider
setDefaultColor(Color) - Method in class etomica.graphics.ColorScheme
setDefaultDaDef(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
setDefaultFontFamily(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the defaultFontFamily value.
setDefaultLabel(String) - Method in class etomica.graphics.DisplayTextBox: Sets label to the given value if it was not previously set.
setDefaultRotation() - Method in class g3dsys.control.G3DSys: Rescales slab and depth after image shell mode is toggled or the number of layers changed.
setDeformation(double) - Method in class etomica.modules.droplet.ConfigurationDroplet
setDegeneracy(int[]) - Method in class etomica.math.discrete.PermutationDegenerateIterator: Invokes setDegeneracy(degeneracy, degeneracy.length), thus using all elements of given array.
setDegeneracy(int[], int) - Method in class etomica.math.discrete.PermutationDegenerateIterator: Sets parameter that describes number of duplicate elements in the iterates.
setDelayExponent(double) - Method in class etomica.graphics.DeviceDelaySlider
setDeltaCut(double) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizable
setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
setDeltaTmax(int) - Method in class etomica.zeolite.MSDProcessor: Allows for a new value of deltaTmax.
setDeltaX(double) - Method in class etomica.util.HistogramExpanding
setDenominator(int) - Method in interface etomica.graph.model.Coefficient
setDenominator(int) - Method in class etomica.graph.model.impl.CoefficientImpl
setDensity(double) - Method in class etomica.box.Box
setDensityProfileDump(IEtomicaDataSource) - Method in class etomica.data.DataProcessorChemicalPotential
setDepth(double) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Set depth percentage
setDepth(double) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Set depth percentage
setDepth(int) - Method in class org.jmol.util.GData: clipping from the front and the back
setDepthPercent(float) - Method in class g3dsys.control.G3DSys
setDescription(JTextArea) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setDescription(JTextArea) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setDestination(IVector) - Method in class etomica.action.MoleculeActionTranslateTo
setDestinationType(DestinationType) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the destinationType attribute value.
setDiagram(int) - Method in class etomica.virial.ClusterSumStickyEF
setDiagramSampling(boolean) - Method in class etomica.virial.cluster.ClusterDiagramTree
setDiameter(String, double) - Method in class etomica.atom.DiameterHashByElement
setDiameter(String, double) - Method in class etomica.atom.DiameterHashByElementType
setDiameter(IAtomType, double) - Method in class etomica.atom.DiameterHashByType
setDiameterHash(DiameterHash) - Method in class etomica.graphics.DisplayBox: Sets the DiameterHash used by this DisplayBox.
setDielectric(double) - Method in class etomica.potential.P2ReactionFieldDipole: Sets the dielectric constant of the fluid surrounding the cavity.
setDielectric(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated: Sets the dielectric constant of the fluid surrounding the cavity.
setDiffusePercent(int) - Static method in class org.jmol.util.GData: df in I = df * (N dot L) + sf * (R dot V)^p
setDim(Dimension) - Method in class etomica.units.UnitGraphics
setDimension(Dimension) - Method in class etomica.data.DataInfoFactory: Sets the dimension
setDimension(Dimension) - Method in interface etomica.data.IEtomicaDataInfoFactory: Sets the dimension
setDimensions(int, int, int, int, int, int, double, double, double, double, double, double) - Method in class etomica.config.GrainBoundaryConfiguration
setDimensions(IVector) - Method in class etomica.lattice.CellLattice
setDimensions(Tensor) - Method in class etomica.space.BoundaryDeformablePeriodic: Sets the boundary tensor to equal the given tensor.
setDims(int[]) - Method in class etomica.modules.rheology.MeterNormalStress
setDimx(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
setDimy(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
setDipole(double) - Method in class etomica.potential.P2HSDipole
setDipole(double) - Method in class etomica.potential.P2LJDipole
setDipoleMomentSquare(double) - Method in class etomica.rotation.P2LJDipole
setDipoleSource(DipoleSource) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
setDipoleSource(DipoleSource) - Method in class etomica.potential.P1ExternalField
setDipoleSource(DipoleSource) - Method in class etomica.potential.P2ReactionFieldDipole: Sets the dipole source used by this object should use.
setDipoleSource(DipoleSource) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated: Sets the dipole source used by this object should use.
setDipoleSource(DipoleSource) - Method in class etomica.potential.PotentialCalculationPhiSum
setDipoleStrength(double) - Method in class etomica.models.water.DipoleSourceWater: Sets the strength (magnitude) of the dipole.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.ApiIntragroup: Specifies the direction, which applies only if iterating pairs with a target atom; otherwise, if all pairs from group are indicated, direction is ignored.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType: Has no effect, but is included as part of the AtomsetIteratorPDT interface.
setDirection(IteratorDirective.Direction) - Method in interface etomica.atom.iterator.AtomsetIteratorDirectable
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.IteratorDirective
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MoleculeIteratorAll: Has no effect, but is included as part of the AtomsetIteratorPDT interface.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MoleculeIteratorMolecule: Has no effect, but is included as part of the AtomsetIteratorPDT interface.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MpiInterspecies1A: Indicates allowed direction for iteration, relative to specified target atom.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MpiIntraspecies1A: Specifies the direction, which applies only if iterating pairs with a target atom; otherwise, if all pairs from group are indicated, direction is ignored.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.MpiMolecule: Specifies the direction from which partners of a target atoms are taken to form iterates.
setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.TripletInnerSequential
setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
setDirection(IteratorDirective.Direction) - Method in class etomica.lattice.RectangularLatticeNbrIterator: Sets the iterator to return only up-list neighbors or down-list neighbors.
setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.cell.Api1ACell: Indicates allowed direction for iteration, relative to specified target atom.
setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.cell.molecule.Mpi1ACell: Indicates allowed direction for iteration, relative to specified target atom.
setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.site.Api1ASite: Indicates allowed direction for iteration, relative to specified target atom.
setDirection(IteratorDirective.Direction) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
setDirection(IVector) - Method in interface etomica.space.IOrientation: Sets the orientation's direction to be the given direction.
setDirection(IVector) - Method in class etomica.space2d.Orientation2D: Sets this orientation to point in the given direction.
setDirection(IVector) - Method in class etomica.space3d.Orientation3D: Sets this orientation to point in the given direction.
setDirection(IVector) - Method in class etomica.space3d.OrientationFull3D: Sets this orientation to point in the given direction.
setDirection(IVectorMutable) - Method in class etomica.spin.P1MagneticField
setDirections(IVector, IVector) - Method in interface etomica.space3d.IOrientationFull3D: Sets the orientation's primary and secondary direction to be the given directions.
setDirections(IVector, IVector) - Method in class etomica.space3d.OrientationFull3D
setDisp(boolean) - Method in class etomica.potential.P2QChemInterpolated
setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
setDistanceToOrigin(double) - Method in class etomica.math.geometry.Plane: Sets perpendicular distance from the plane to the origin.
setDoAdjustOnTime(boolean) - Method in class etomica.overlap.IntegratorOverlap: If true, causes the integrator to optimize how much each system runs based on the wall clock time needed to run steps in each system.
setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfiguration: Directs the writer to apply periodic boundary conditions or not (true by default).
setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationBinary: Directs the writer to apply periodic boundary conditions or not (true by default).
setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationDLPOLY: Directs the writer to apply periodic boundary conditions or not (true by default).
setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationP2DLPOLY: Directs the writer to apply periodic boundary conditions or not (true by default).
setDoApplyPBC(boolean) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
setDoApplyPBC(boolean) - Method in class etomica.nbr.cell.NeighborCellManager
setDoApplyPBC(boolean) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
setDoApplyPBC(boolean) - Method in class etomica.nbr.list.NeighborListManager
setDoAveraging(boolean) - Method in class etomica.util.HistogramNotSoSimple: turns "averaging" on or off.
setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoft
setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoftBD
setDoClear(boolean) - Method in class etomica.graphics.DisplayPlot
setDoConfigButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic: Enable the config (and velocity) buttons.
setDoCov(boolean) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
setDoDensityInput(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic: Enable the RDF plot.
setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoDouble(boolean) - Method in class etomica.modules.rheology.MeterNormalStress
setDoDrawLines(DataTag[], boolean) - Method in class etomica.graphics.DisplayPlot: Sets the data set corresponding to the given tags to be have the data points connected with lines or not.
setDoEnforceBounds(boolean) - Method in class etomica.data.DataSourceUniform
setDoExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoExchange(boolean[]) - Method in class etomica.virial.MCMoveChangeBondLength
setDoExchange(boolean[]) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
setDoExchangeCondensing(boolean) - Method in class etomica.virial.cluster.VirialDiagrams: Turn on replacement of exchanged groups of nodes with a single node (of a different color)
setDoExchangeCondensing(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT: Turn on replacement of exchanged groups of nodes with a single node (of a different color)
setDoExchangeF(boolean) - Method in class etomica.virial.cluster.VirialDiagrams: Turn on replacement of eBonds with bonds that represent a single fBond between an exchange group and another molecule (or another exchange group).
setDoExchangeF(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT: Turn on replacement of eBonds with bonds that represent a single fBond between an exchange group and another molecule (or another exchange group).
setDoExcludeBogusConfigs(boolean) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
setDoExcludeBogusConfigs(boolean) - Method in class etomica.virial.MeterVirialBinMultiThreaded
setDoExcludeNonNeighbors(boolean) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert: Configures the move to not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
setDoExcludeNonNeighbors(boolean) - Method in class etomica.normalmode.MCMoveAtomCoupled: Configures the move to not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
setDoExcludeNonNeighbors(boolean) - Method in class etomica.normalmode.MCMoveMoleculeCoupled: Configures the move to not explicitly calculate the potential for atom pairs that are not neighbors (as determined by the potentialMaster).
setDoExp(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoFastButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
setDoHB(boolean) - Method in class etomica.virial.cluster.VirialDiagrams: Enable construction of diagrams from the Hellmann-Bich formulation
setDoHB(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT: Enable construction of diagrams from the Hellmann-Bich formulation
setDoIncludeACInError(boolean) - Method in class etomica.data.AccumulatorAverage: Include correction to the uncertainty from block correlation function as prescribed in Kolafa, Jiri(1986) 'Autocorrelations and subseries averages in Monte Carlo Simulations', Molecular Physics (59) 1035
setDoIncludeCoefficients(boolean) - Method in class etomica.graph.viewer.GraphMap
setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoLegend(boolean) - Method in class etomica.graphics.DisplayPlot: Mutator for flag determining if a legend is to be shown.
setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagrams: Only include graphs with nonadditive bonds.
setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoMultiFromPair(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoMultiFromPair(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoNegativeExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoNegativeExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoNMoleculeSlider(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic: Enable the # of molecules slider.
setDoNonEquilibrium(boolean) - Method in class etomica.potential.PotentialCalculationPressureTensor
setDoPBC(boolean) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
setDoPBC(boolean) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
setDoRDF(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic: Enable the RDF plot.
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoReeHoover(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
setDoResetFilter(boolean) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
setDoScaling(boolean) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setDoSecondDerivative(boolean) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
setDoShortcut(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
setDoShortcut(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
setDoShowCurrent(boolean) - Method in class etomica.graphics.DisplayTextBoxesCAE
setDoStrictBlockData(boolean) - Method in class etomica.data.AccumulatorAverageFixed: Sets the accumulator to base statistics only on block data (where that makes sense).
setDoWiggle(boolean) - Method in class etomica.virial.simulations.SimulationVirial
setDoWiggle(boolean) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setDrawable(boolean) - Method in class g3dsys.images.Figure
setDrawable(boolean) - Method in class g3dsys.images.ImageShell
setDrawBoundary(int) - Method in class etomica.graphics.DisplayCanvas
setDrawBoundaryType(int) - Method in class g3dsys.images.ImageShell: Sets the boundary drawing style
setDrawingHeight(int) - Method in class etomica.graphics.DisplayBox: Set the height of the drawing area (only relevant for 1D)
setDrawingThickness(int) - Method in class etomica.potential.P1HardBoundary
setDrawNumbersOfBlack(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
setDrawNumbersOfWhite(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
setDrawOverflow(boolean) - Method in class etomica.graphics.DisplayBox
setDrawPoints(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
setDsABase(double) - Method in class etomica.models.oneDHardRods.MeterOverlap
setDsABase(double) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
setDsBBase(double) - Method in class etomica.models.oneDHardRods.MeterOverlap
setDsBBase(double) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
setDst(File) - Method in class etomica.graph.view.rasterizer.SVGConverter: When converting a single source, dst can be a file.
setDSVO(DataSourceVirialOverlap) - Method in class etomica.virial.overlap.IntegratorOverlap: Sets the DataSource that retrieves data from both boxs and provides information to the integrator about their progress.
setDv(double) - Method in class etomica.modules.droplet.P2Cohesion
setEdgeLength(double) - Method in class etomica.math.geometry.Cube
setEdgeLength(double) - Method in class etomica.math.geometry.Square
setEdgeLength(double) - Method in class etomica.math.geometry.TruncatedOctahedron: Specifies the common length of all edges of the truncated octahedron.
setEdgeLengths(IVector) - Method in class etomica.math.geometry.Cuboid: Sets the three edge lengths of the cuboid, taking each element of the given vector for the length of the corresponding cuboid edge.
setEdgeLengths(double, double, double) - Method in class etomica.math.geometry.Cuboid: Sets the lengths of all edges of the cuboid.
setEdgeLengths(IVector) - Method in class etomica.math.geometry.LineSegment: Sets the length equal to the element of the (presumably 1D) vector.
setEdgeLengths(IVector) - Method in class etomica.math.geometry.Rectangle: Sets the two edge lengths of the rectangle, taking each element of the given vector for the length of the corresponding rectangle edge.
setEdgeLengths(double, double) - Method in class etomica.math.geometry.Rectangle
setEdgeLengths(IVector) - Method in interface etomica.math.geometry.Rectangular: Specifies the D edge lengths needed to describe the shape of the polytope.
setEdgeVector(int, IVector) - Method in class etomica.space.BoundaryDeformablePeriodic
setEdgeVectors(IVector[]) - Method in class etomica.math.geometry.Parallelepiped: Sets the lengths and directions of all edges of the parellelepiped.
setEdgeVectors(IVector[]) - Method in class etomica.math.geometry.Parallelogram: Sets the lengths and directions of all edges of the parellelepiped.
setEdgeVectors(IVector[]) - Method in interface etomica.math.geometry.Parallelotope: Specifies the polytope via an array of edge vectors.
setEditable(boolean) - Method in class etomica.graphics.DeviceBox
setEditValues(boolean) - Method in class etomica.graphics.DeviceSlider
setEditValues(boolean) - Method in class etomica.graphics.DeviceThermoSlider: Set whether the temperature text box should be editable.
setEditValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set whether the temperature text box should be editable.
setEditValues(boolean) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set whether the x- and y-Cell # text box should be editable.
setEditValues(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set whether the eigenvalue # text box should be editable.
setEditValues(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set whether the wavevector # text box should be editable.
setEditVariables(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setEditVariables(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes: Informs the move of the eigenvectors for the selected wave vector.
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV: Informs the move of the eigenvectors for the selected wave vector.
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV: Informs the move of the eigenvectors
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterF
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setEigenVectors(double[][][]) - Method in class etomica.normalmode.IntegratorHarmonic
setEigenVectors(double[][][]) - Method in class etomica.normalmode.MCMoveHarmonic
setEigenVectors(double[][]) - Method in class etomica.normalmode.MCMoveHarmonicStep: Informs the move of the eigenvectors for the k=0 wave vector.
setEigenVectors(double[][][]) - Method in class etomica.normalmode.MCMoveSingleMode: Informs the move of the eigenvectors for the selected wave vector.
setEigenvectors(double[]) - Method in class etomica.normalmode.MeterHarmonicCoordinate
setEigenvectors(double[][][]) - Method in class etomica.normalmode.MeterHarmonicEnergy
setEigenvectors(double[][][]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
setElement(IElement) - Method in class etomica.chem.models.ModelChain: Sets the Element used for the leaf atoms in the chain.
setElement(int, int, float) - Method in class org.jmol.util.Matrix3f: Sets the specified element of this matrix3d to the value provided.
setElement(int, int, float) - Method in class org.jmol.util.Matrix4f: Sets the specified element of this matrix4f to the value provided.
setEllipsoidMatrix(Vector3f[], float[], Vector3f, Matrix3f) - Static method in class org.jmol.util.Quadric
setEnabled(boolean) - Method in interface etomica.api.IPotentialMaster: Permits enabling/disabling of all potentials.
setEnabled(IPotentialMolecular, boolean) - Method in interface etomica.api.IPotentialMaster: Indicates that the specified potential should not contribute to potential calculations.
setEnabled(IPotentialAtomic, boolean) - Method in interface etomica.api.IPotentialMaster: Indicates that the specified potential should not contribute to potential calculations.
setEnabled(boolean) - Method in class etomica.graphics.DeviceNSelector
setEnabled(boolean) - Method in class etomica.graphics.DeviceSlider: Sets the deivce's slider and textfield to be enabled or not.
setEnabled(IPotentialAtomic, boolean) - Method in class etomica.potential.PotentialGroup: Indicates that the specified potential should not contribute to potential calculations.
setEnabled(boolean) - Method in class etomica.potential.PotentialMaster
setEnabled(IPotentialMolecular, boolean) - Method in class etomica.potential.PotentialMaster
setEnabled(IPotentialAtomic, boolean) - Method in class etomica.potential.PotentialMaster
setEnabled(boolean) - Method in class etomica.potential.PotentialMasterLrc
setEnabled(boolean) - Method in class etomica.util.Grabber.ActionCornerSetter
setEnabled(boolean) - Method in class etomica.util.Grabber.DefaultMouseListener
setEnablePBC(boolean) - Method in class etomica.models.nitrogen.P2Nitrogen
setEnd(Point3f) - Method in class g3dsys.images.Line
setEnd(float, float, float) - Method in class g3dsys.images.Line
setEnergyBase(double) - Method in class etomica.normalmode.BoltzmannProcessor
setEnergyFac(double) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingRegrow: sets the harmonic bond "energy" factor The probability of the bond have length x is proportional to exp(-factor*x^2) (there is no temperature involved here)
setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange: sets the harmonic bond "energy" factor The probability of the bond to have length x is proportional to exp(-factor*x^2) (there is no temperature involved here)
setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingScale
setEnergyMeter(MeterPotentialEnergy) - Method in class etomica.data.meter.MeterWidomInsertion
setEnergyMeter(MeterPotentialEnergy, MeterPotentialEnergy) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
setEnergyMeter(MeterPotentialEnergy) - Method in class etomica.liquidLJ.MeterWidomInsertionP
setEpsilon(double) - Method in class etomica.modules.adsorption.EOSSW
setEpsilon(double) - Method in class etomica.modules.adsorption.P1Wall
setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.colloid.P1Wall
setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
setEpsilon(double) - Method in class etomica.modules.droplet.P2Cohesion
setEpsilon(double) - Method in class etomica.modules.mu.P2SquareWellOneSide: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
setEpsilon(double) - Method in class etomica.modules.rosmosis.P1Tether
setEpsilon(double) - Method in class etomica.modules.sam.P1WCAWall
setEpsilon(double) - Method in class etomica.modules.vle.VLESim
setEpsilon(double) - Method in class etomica.potential.P22CLJQ
setEpsilon(double) - Method in class etomica.potential.P2Exp6Buckingham
setEpsilon(double) - Method in class etomica.potential.P2HardAssociation: Accessor method for depth of well.
setEpsilon(double) - Method in class etomica.potential.P2HardAssociationCone: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2LennardJones: Mutator method for Lennard-Jones energy parameter
setEpsilon(double) - Method in class etomica.potential.P2LennardJonesDreiding: Mutator method for Lennard-Jones energy parameter
setEpsilon(double) - Method in class etomica.potential.P2LJDipole
setEpsilon(double) - Method in class etomica.potential.P2LJQ
setEpsilon(double) - Method in class etomica.potential.P2LJQQ
setEpsilon(double) - Method in class etomica.potential.P2ModifiedMorse
setEpsilon(double) - Method in class etomica.potential.P2Morse
setEpsilon(double) - Method in class etomica.potential.P2PenetrableSphere: Accessor method for height of core.
setEpsilon(double) - Method in class etomica.potential.P2PenetrableSquareWell: Mutator method for depth of well.
setEpsilon(double) - Method in class etomica.potential.P2SoftSphere: Mutator method for soft-sphere energy parameter
setEpsilon(double) - Method in class etomica.potential.P2SquareWell: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2SquareWellRobust: Accessor method for depth of well
setEpsilon(double) - Method in class etomica.potential.P2TriangleWell
setEpsilon(double) - Method in class etomica.potential.P2WCA: Mutator method for the energy parameter
setEpsilon(double) - Method in class etomica.potential.P3BondAngle: Sets the characteristic energy of the potential
setEpsilon(double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig: Sets the characteristic energy of the potential
setEpsilon(double) - Method in class etomica.rotation.P2LJDipole
setEpsilon(double) - Method in class etomica.units.systems.LJ
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
setEpsilon(double) - Method in class etomica.yukawa.P2HC2Yukawa: Mutator methods for size and energy parameters.
setEpsilon6(double) - Method in class etomica.potential.P2Exp6Buckingham
setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
setEpsilonCG(double) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
setEpsilonCore(double) - Method in class etomica.potential.P2DoubleWell: Accessor method for depth of well
setEpsilonCore(double) - Method in class etomica.potential.P2PenetrableSquareWell: Sets height of penetrable core.
setEpsilonNR(double) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
setEpsilonWell(double) - Method in class etomica.potential.P2DoubleWell
setEpsInner(double) - Method in class etomica.potential.P2PenetrableBond
setEpsOuter(double) - Method in class etomica.potential.P2PenetrableBond
setEquilibrating(boolean) - Method in class etomica.integrator.mcmove.MCMoveManager
setErrMulti(double) - Method in class etomica.potential.P2HePCKLJS
setEthanolParams(int) - Static method in class etomica.models.rowley.EthanolRouteParams
setEValNum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the current value for the eigenvalue # slider/text box.
setEValNum(int) - Method in class etomica.normalmode.IntegratorHarmonic
setEventInterval(int) - Method in class etomica.integrator.Integrator: Sets value of interval between successive firing of integrator interval events.
setExcludeArticulationPair(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to exclude clusters having an articulation pair.
setExcludeArticulationPoint(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to exclude clusters having an articulation point.
setExcludeNodalPoint(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to exclude clusters having a nodal point.
setExecuteOnload(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets whether or not scripts attached to the DOM using 'onload' event attribute must be executed before rasterizing.
setExp(int) - Method in class etomica.virial.MayerSSSeries: Sets the HS diameter.
setExpGroupingSize(int) - Method in class etomica.util.ScientificFormat
setExpMaximumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
setExpMinimumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
setExpNegativePrefix(String) - Method in class etomica.util.ScientificFormat
setExpNegativeSuffix(String) - Method in class etomica.util.ScientificFormat
setExponentialMode() - Method in class etomica.util.ScientificFormat
setExpPositivePrefix(String) - Method in class etomica.util.ScientificFormat
setExpPositiveSuffix(String) - Method in class etomica.util.ScientificFormat
setExpPSpan(double) - Method in class etomica.normalmode.MeterDDP
setExpPSpan(double) - Method in class etomica.normalmode.MeterDP
setExternalField(IVector) - Method in class etomica.potential.P1ExternalField
setExtraData(IEtomicaDataSource) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins: Sets a data source used to draw an extra set of "atoms".
setExtraTargetClusters(ClusterAbstract[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setFactory(SimulationRunner) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
setFalseLabel(String) - Method in class etomica.action.ActionToggle: Specifies the button's label when the toggle is set to false.
setFalseLabel(String) - Method in class etomica.graphics.DeviceToggleButton: Specifies the button's label when the toggle is set to false.
setFalseLabel(String) - Method in class etomica.graphics.DeviceToggleRadioButtons: Specifies the button's label when the toggle is set to false.
setFile(File) - Method in class etomica.action.PDBWriter: Sets the file to write to.
setFile(File) - Method in class etomica.action.XYZWriter: Sets the file to write to.
setFile(String) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
setFile(String) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
setFileName(String) - Method in class etomica.action.PDBWriter: Sets the file name to write to.
setFileName(String) - Method in class etomica.action.WriteConfiguration
setFileName(String) - Method in class etomica.action.WriteConfigurationBinary
setFileName(String) - Method in class etomica.action.XYZWriter: Sets the file name to write to.
setFileName(String) - Method in class etomica.data.DataLogger: Define the name of the output file.
setFileName(String) - Method in class etomica.dimer.IntegratorDimerMin: Set's the filename of the output of this integrator.
setFileName(String) - Method in class etomica.dimer.IntegratorDimerRT: Set's the filename of the output of this integrator.
setFilename(String) - Method in class etomica.models.oneDHardRods.WriteHistograms
setFileName(String) - Method in class etomica.normalmode.NormalModesMolecular
setFileName(String) - Method in class etomica.normalmode.NormalModesPotential
setFilename(String) - Method in class etomica.normalmode.WriteS
setFileWriter(FileWriter) - Method in class etomica.data.DataArrayWriter
setFileWriter(FileWriter) - Method in interface etomica.data.DataLogger.DataWriter: Sets the FileWriter to be used for actual file I/O.
setFileWriter(FileWriter) - Method in class etomica.data.DataTableWriter
setFilter(AtomFilter) - Method in class etomica.modules.droplet.MeterDeformation
setFitToWindow(boolean) - Method in class etomica.graphics.DisplayTable: If true, columns will be squeezed so table fits to window; if false, table will exceed window size, and to view full width must be placed in a scroll pane.
setFixedCOM(boolean) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
setFixedDaDef(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
setFixedDeltaU(double) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
setFixedOrientation(boolean) - Method in class etomica.virial.MCMoveChangeBondLength
setFixedSpecies(ISpecies) - Method in class etomica.config.GrainBoundaryTiltConfiguration
setFixedWall(FixedWall) - Method in class etomica.interfacial.IntegratorFixedWall
setFlexCancelOnly(boolean) - Method in class etomica.virial.cluster.VirialDiagrams: This method only effects the graphs returned by getMSMCGraphs
setFlexCancelOnly(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT: This method only effects the graphs returned by getMSMCGraphs
setFlexibleMode() - Method in class etomica.util.ScientificFormat
setFluctuationFactor(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
setFluidNbrDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
setFont(JmolFont) - Method in class org.jmol.g3d.Graphics3D
setFont(JmolFont) - Method in class org.jmol.util.GData
setFontFid(byte) - Method in class org.jmol.g3d.Graphics3D
setFontFid(byte) - Method in class org.jmol.util.GData
setForce(double) - Method in class etomica.potential.P1HardMovingBoundary
setForceconstant(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setForceconstant(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setForceSum(PotentialCalculationForceSum) - Method in class etomica.integrator.IntegratorVelocityVerlet
setForceSum(PotentialCalculationForceSum) - Method in class etomica.integrator.IntegratorVelocityVerletShake
setFrac(double) - Method in class etomica.normalmode.MCMoveHarmonicEin: Sets the fraction of the systems energy from the normal mode contribution.
setFrac(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic: Sets the fraction that the system is coupled to measured energy.
setFrac(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
setFrac(double) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setFrac(double) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setFrameProperties() - Method in class etomica.virial.GUI.containers.AppFrameMixtureBuilder
setFreeRadicalColor(IAtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
setFrequency(MCMove, double) - Method in class etomica.integrator.mcmove.MCMoveManager: Sets the trial frequency for the given move to the given frequency.
setFugacityFraction(double[]) - Method in class etomica.integrator.mcmove.MCMoveSemigrand: Specifies the fugacity fractions for the set of species that can participate in an exchange move.
setFullBondColor(IAtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
setFullColor(IAtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
setFunction(IFunction) - Method in class etomica.data.DataSourceFunction
setFunction(FunctionInvertible) - Method in class etomica.modifier.ModifierFunctionWrapper
setFunction(FunctionMultiDimensionalDifferentiable) - Method in class etomica.util.numerical.Function1d
setG(double) - Method in class etomica.modules.droplet.P1Smash
setG1(Graph) - Method in class etomica.graph.isomorphism.AbstractSearchState
setG2(Graph) - Method in class etomica.graph.isomorphism.AbstractSearchState
setGamma(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
setGamma(double) - Method in class etomica.potential.P3BondAngleDreiding: Sets the characteristic energy of the potential
setGammaPositionAndOrientation(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setGBplane(int[]) - Method in class etomica.config.GrainBoundaryTiltConfiguration: Allows a user to specify a plane for GB
setGlobal() - Method in class org.jmol.script.ScriptVariable
setGlobalMoveInterval(double) - Method in class etomica.integrator.IntegratorManagerMC: Sets the average interval between box-swap trials.
setGoal(int) - Method in class etomica.graph.traversal.AbstractTraversal
setGreyscaleMode(boolean) - Method in class org.jmol.util.GData: controls greyscale rendering
setGroupingSize(int) - Method in class etomica.util.ScientificFormat
setGroupingUsed(boolean) - Method in class etomica.util.ScientificFormat
setH(double) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
setH(double) - Method in class etomica.spin.P1MagneticField
setH(double) - Method in class etomica.util.numerical.FiniteDifferenceDerivative
setHardCoreDiamterSq(double) - Method in class etomica.potential.P22CLJQ
setHardCoreDiamterSq(double) - Method in class etomica.potential.P2LJQ
setHardCoreDiamterSq(double) - Method in class etomica.rotation.P2LJDipole
setHarmonicFudge(double) - Method in interface etomica.normalmode.NormalModes: Set the fudge factor applied to frequencies.
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes1DHR
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes2D
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes3D
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesFromFile
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesMolecular
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesPotential
setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesSoftSpherical
setHarmonicFudge(double) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
setHarmonicPressure(double[], double) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
setHarmonicWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
setHarmonicWV(int) - Method in class etomica.normalmode.MCMoveSingleMode: The harmonic wavevector and all wavevectors with higher numbers are not able to be changed by this MCMove.
setHashMapAtomsetIterator(HashMap<String[], AtomsetIteratorBasisDependent>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setHashMapAtomTypeLikePairs(HashMap<String[], IAtomType[]>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setHashMapAtomTypesUnlikePairs(HashMap<String[], IAtomType[]>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
setHashMapPotentialIntraBonded(HashMap<String[], IPotential>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
setHashMapPotentialNonBonded(HashMap<String[], IPotential>) - Method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
setHeight(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: In less than or equal to zero, the height is not constrained on the output image.
setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterElongation
setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterStrain
setHexagonal(boolean) - Method in class etomica.modules.materialfracture.StrainColorScheme
setHistogram(Histogram) - Method in class etomica.data.AccumulatorHistogram
setHistogram(Histogram) - Method in class etomica.models.oneDHardRods.WriteHistograms
setHistogramming(boolean) - Method in class etomica.virial.cluster.ClusterDiagramTree
setHistory(History) - Method in class etomica.data.AccumulatorHistory
setHistoryLength(int) - Method in interface etomica.util.History: Sets the number of data points to be tracked by the History.
setHistoryLength(int) - Method in class etomica.util.HistoryCollapsing: Sets the number of values kept in the history.
setHistoryLength(int) - Method in class etomica.util.HistoryComplete: Sets the number of values kept in the history.
setHistoryLength(int) - Method in class etomica.util.HistoryScrolling: Sets the number of values kept in the history.
setHOptimizer(boolean) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
setId(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
setID(int) - Method in class g3dsys.images.Figure: Set the ID of the figure.
setIdentity() - Method in class org.jmol.util.Matrix3f: Sets this Matrix3f to identity.
setIdentity() - Method in class org.jmol.util.Matrix4f: Sets this Matrix4f to identity.
setIgnoredAtomType(IAtomType) - Method in class etomica.modules.chainequilibrium.MeterChainLength
setIgnoreOverlap(boolean) - Method in class etomica.action.IntegratorReset
setIgnoreOverlap(boolean) - Method in class etomica.action.SimulationRestart
setIgnoreOverlap(boolean) - Method in class etomica.zeolite.ZeoliteSimStart
setIgnoreReferenceAvg(boolean) - Method in class etomica.virial.overlap.DataVirialOverlap: Directs this class to ignore the reference average when deciding how much time to spend on each system.
setImage(Image) - Method in class etomica.util.Grabber.ImagePanel
setImageShells(int) - Method in class etomica.graphics.DisplayBox: Changes the value of image shells, and increases/decreases scale accordingly.
setImax(int) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
setImportantAtoms() - Method in class etomica.action.IntegratorDimerApproach
setIncludeAdiabatic(boolean) - Method in class etomica.graphics.DeviceThermoSelector
setIncludeHeader(boolean) - Method in class etomica.data.DataArrayWriter: Directs the writer to include column headers or not
setIncludeHeader(boolean) - Method in class etomica.data.DataTableWriter: Directs the writer to include column headers or not
setIncludeLrc(boolean) - Method in class etomica.atom.iterator.IteratorDirective: Sets flag indicating if lrc potentials (long-range correction) should be included.
setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterHyperVirial: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPotentialEnergy: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressure: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressureMolecular: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressureTensor: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.liquidLJ.MeterPU: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.modules.vle.MeterPressure2: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.normalmode.MeterPressureSuperBox: Sets flag indicating whether calculated energy should include long-range correction for potential truncation (true) or not (false).
setIncludeLrc(boolean) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
setIncludeLrc(boolean) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
setIncludeLrc(boolean) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setIncludeLrc(boolean) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setIndex(int) - Method in interface etomica.api.IAtom: Informs the IAtom of its index, which is used to construct the address.
setIndex(int) - Method in interface etomica.api.IAtomType: Informs the ISpecies what its index should be.
setIndex(int) - Method in interface etomica.api.IBox: Informs the IBox what its index is.
setIndex(int) - Method in interface etomica.api.IMolecule: Informs the IMolecule of its index.
setIndex(int) - Method in interface etomica.api.ISpecies: Informs the ISpecies what its index should be.
setIndex(int) - Method in class etomica.atom.Atom
setIndex(int) - Method in class etomica.atom.AtomTypeLeaf
setIndex(int) - Method in class etomica.atom.Molecule
setIndex(int) - Method in class etomica.box.Box
setIndex(int) - Method in class etomica.species.Species
setIndexed(int) - Method in class etomica.graph.view.rasterizer.SVGConverter: Tells the PNG encoder to reduce the image to 256 colors, so the PNG file is indexed.
setIndexSelectedSpecies(int) - Method in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
setInflateDimensions(boolean[]) - Method in class etomica.data.meter.MeterPressureByVolumeChange: For anisotropic volume change, indicates dimension in which volume is perturbed.
setInflater(BoxInflate) - Method in class etomica.integrator.mcmove.MCMoveVolume
setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
setInitialStateConditions(double, double) - Method in class etomica.kmc.IntegratorKMC
setInitialStateConditions(double, double) - Method in class etomica.kmc.IntegratorKMCCluster
setInitVolume(IVector) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
setInitVolume(IVector) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
setInnerIterator(GraphIterator) - Method in class etomica.graph.iterators.CartesianIterator
setInnerList(IAtomList) - Method in class etomica.atom.iterator.ApiInterArrayList: Sets the list that will be used to generate the pairs.
setInnerList(IMoleculeList) - Method in class etomica.atom.iterator.MpiInterArrayList: Sets the list that will be used to generate the pairs.
setInnerPermutator(DefaultPermutator) - Method in class etomica.graph.iterators.CartesianPermutator
setInnerWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
setInnerWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeSW
setInputData(double[], double[]) - Method in class etomica.util.numerical.AkimaSpline
setInputData(double[], double[], double[]) - Method in class etomica.util.numerical.AkimaSplineSmoother
setInputData(double[], double[], double[]) - Method in class etomica.util.numerical.AkimaSplineSmootherDy
setInputData(double[], double[], double[], double[]) - Method in class etomica.util.numerical.AkimaSplineSmootherDy: Set the nominal values for x and y and uncertainty in y (ey).
setInputFileName(String) - Method in class etomica.util.ReadParameters: Sets the fileName to read the parameters from.
setInputFileName(String) - Method in class etomica.util.WriteParameters: Sets the fileName to read the parameters from.
setInt(int) - Method in class org.jmol.util.Rgb16
setInteger(boolean) - Method in class etomica.graphics.DeviceBox: Sets a flag indicating if the value should be displayed as an integer.
setIntegerDisplay(boolean) - Method in class etomica.graphics.DisplayTextBox
setIntegrationParameters(double, double, double, double, int, int) - Method in class etomica.models.oneDHardRods.DoubleIntegralEtas
setIntegrator(IIntegrator) - Method in interface etomica.action.IntegratorAction
setIntegrator(IIntegrator) - Method in class etomica.action.IntegratorActionAdapter
setIntegrator(IntegratorBox) - Method in class etomica.data.DataProcessorChemicalPotential
setIntegrator(IntegratorHard) - Method in class etomica.data.DataSourceCountCollisions
setIntegrator(IIntegrator) - Method in class etomica.data.DataSourceCountSteps
setIntegrator(IntegratorMD) - Method in class etomica.data.DataSourceCountTime
setIntegrator(IntegratorBox) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor: Sets the integrator.
setIntegrator(IntegratorHard) - Method in class etomica.data.DataSourceTensorVirialHard: Informs meter of the integrator for its box, and zeros elapsed-time counter
setIntegrator(IntegratorMD) - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressure: Sets the integrator associated with this instance.
setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressureByVolumeChange: Sets the integrator associated with this instance.
setIntegrator(IntegratorHard) - Method in class etomica.data.meter.MeterPressureHard: Registers meter as a collisionListener to the integrator, and sets up a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorHard) - Method in class etomica.data.meter.MeterPressureHardTensor
setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressureMolecular: Sets the integrator associated with this instance.
setIntegrator(IntegratorVelocityVerlet) - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterWidomInsertion: Sets the integrator associated with this class.
setIntegrator(IntegratorBox) - Method in class etomica.graphics.DeviceThermoSelector
setIntegrator(IntegratorBox) - Method in class etomica.liquidLJ.MeterWidomInsertionP: Sets the integrator associated with this class.
setIntegrator(IntegratorVelocityVerlet) - Method in class etomica.meam.DataProcessorCvMD
setIntegrator(IntegratorHard) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis: Registers meter as a collisionListener to the integrator, and sets up a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorHard) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
setIntegrator(IntegratorHard) - Method in class etomica.modules.mu.DataSourceWallPressureMu: Registers meter as a collisionListener to the integrator, and sets up a DataSourceTimer to keep track of elapsed time of integrator.
setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterNormalStress
setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterViscosity
setIntegrator(IntegratorBox) - Method in class etomica.modules.rosmosis.MeterFlux
setIntegrator(IntegratorHarmonic) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Sets the integrator for the device.
setIntegrator(IntegratorHarmonic) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Sets the integrator for the device.
setIntegrator(IntegratorBox) - Method in class etomica.normalmode.MeterPressureSuperBox: Sets the integrator associated with this instance.
setIntegrator(IntegratorBox) - Method in class etomica.potential.PotentialCalculationPressureTensor: Sets an integrator to use a source for the temperature to compute the kinetic portion of the pressure.
setIntegrator(IIntegrator) - Method in class etomica.zeolite.MSDCoordWriter
setIntegratorMC(IntegratorMC, int) - Method in class etomica.integrator.IntegratorMD
setIntegratorOverlap(IntegratorOverlap) - Method in class etomica.normalmode.SimOverlapModule
setIntegrators(IntegratorMC, IntegratorMD, IRandom) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
setIntegrators(IntegratorBox, IntegratorBox) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Sets the integrator for the device.
setInteractionRange(double) - Method in class etomica.nbr.CriterionPositionWall: Informs the criterion of the interaction range of the wall potential.
setInteractionRange(double) - Method in class etomica.nbr.CriterionSimple
setInteractionRange(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
setIntercepts(double, double, double) - Method in class etomica.math.geometry.Plane: Reorients and positions the plane so that its intercepts with the x-, y-, and z-axes are the given values, respectively.
setInteriorColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
setInterval(long) - Method in class etomica.data.DataPumpListener
setInterval(int) - Method in class etomica.listener.IntegratorListenerAction
setInterval(int) - Method in class etomica.listener.IntegratorListenerGroupSeries
setIntraMolecular(boolean) - Method in class etomica.nbr.CriterionMolecular: Configures to accept intra- (if argument is true) or inter- (if argument is false) molecular pairs.
setIntraMolecularCriterion(NeighborCriterion) - Method in class etomica.nbr.CriterionInterMolecular: Configures to use the given criterion for intramolecular pairs.
setInverseNormixes() - Static method in class org.jmol.util.Normix
setIs256() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
setIs864() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
setIsAlpha() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setIsAlpha() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setIsAppend(boolean) - Method in class etomica.action.XYZWriter
setIsBeta() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setIsBetaHCP() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setIsBetaLatticeSum() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setIsDoLatticeSum() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheres
setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresCustom
setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresHetero
setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresMono
setIsFluctuationFromAvg(boolean) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
setIsGamma() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setIsGamma() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setIsInteracting(boolean, int) - Method in class etomica.nbr.list.AtomPotentialList: Sets whether the atom is interacting or not with the potential corresponding to the given index.
setIsInteracting(boolean, int) - Method in class etomica.nbr.list.molecule.MoleculePotentialList: Sets whether the molecule is interacting or not with the potential corresponding to the given index.
setIsothermal() - Method in class etomica.graphics.DeviceThermoSlider: Set the Isothermal button to its selected state.
setIsothermal(boolean) - Method in class etomica.integrator.IntegratorBox
setIsothermal(boolean) - Method in class etomica.integrator.IntegratorMD
setIsothermal(boolean) - Method in class etomica.modules.adsorption.IntegratorHybrid
setIsothermal(boolean) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
setIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the Isothermal button to its selected state.
setIsothermalButtonsVisibility(boolean) - Method in class etomica.graphics.DeviceThermoSlider
setIsothermalButtonsVisibility(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
setIsUpperBound(boolean) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
setIterator(AtomIterator) - Method in class etomica.data.DataSourceRmsVelocity: Sets the iterator defining the atoms for which the RMS velocity is calculated.
setIterator(AtomsetIteratorBoxDependent) - Method in class etomica.data.meter.MeterBondOrderParameterQ: Sets the iterator that gives the atoms over which the order parameter will be calculated.
setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterKineticEnergy: Sets the iterator that defines the atoms which are summed for their total kinetic energy.
setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterLocalDensity
setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterLocalMoleFraction
setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterMeanSquareDisplacement
setIterator(MoleculeIteratorAllMolecules) - Method in class etomica.data.meter.MeterRadiusGyration: Mutator method for the iterator that generates the atom pairs used to tabulate the ROG.
setIterator(AtomIteratorBoxDependent) - Method in class etomica.zeolite.MSDCoordWriter
setJmax(int) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
setJSpinnerCountOfSpecies1(JSpinner, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setK(IVector) - Method in class etomica.lattice.LatticeSum
setK(IVector) - Method in class etomica.lattice.LatticeSumCrystal
setK(IVector) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
setK(IVectorMutable) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
setKappa(double) - Method in class etomica.yukawa.P2Yukawa: Mutator methods for size and energy parameters.
setKinetic(DataSourceScalar) - Method in class etomica.data.meter.MeterEnergy
setKineticEnergyMeter(DataSourceScalar) - Method in class etomica.data.meter.MeterTemperature
setL(int) - Method in class etomica.data.meter.MeterBondOrderParameterQ: Sets the value of the parameter l, to indicate if Q4 or Q6 is to be computed.
setLabel(String) - Method in class etomica.data.DataInfoFactory: Sets the label
setLabel(String) - Method in interface etomica.data.IEtomicaDataInfoFactory: Sets the label
setLabel(String) - Method in class etomica.graphics.DeviceBox: Sets the value of a descriptive label using the given string.
setLabel(String) - Method in class etomica.graphics.DeviceButton: Sets the value of a descriptive label using the given string.
setLabel(String) - Method in class etomica.graphics.DeviceButtonGroup: Sets the label for the group of radio buttons
setLabel(String) - Method in class etomica.graphics.DeviceSelector
setLabel(String) - Method in class etomica.graphics.DeviceSlider: Sets the value of a descriptive label using the given string.
setLabel(String) - Method in class etomica.graphics.DeviceSpinner: Sets the value of a descriptive label using the given string.
setLabel(String) - Method in class etomica.graphics.Display: Accessor method of the label describing the display.
setLabel(String) - Method in class etomica.graphics.DisplayTextBox: Sets the value of a descriptive label using the given string.
setLabel(String) - Method in class etomica.graphics.DisplayTextBoxesCAE
setLabel(String) - Method in class etomica.modifier.ModifierGeneral
setLabel(String) - Method in class etomica.zeolite.DeviceButtonSingle: Sets the value of a descriptive label using the given string.
setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DeviceBox
setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DisplayTextBox
setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DisplayTextBoxesCAE
setLabels(String[]) - Method in class etomica.graphics.DeviceTernarySelector: Labels used to indicate the three component fractions.
setLabelType(DeviceBox.LabelType) - Method in class etomica.graphics.DeviceBox: Sets the label type to "border" or "string".
setLabelType(DisplayTextBox.LabelType) - Method in class etomica.graphics.DisplayTextBox
setLabelType(DisplayTextBox.LabelType) - Method in class etomica.graphics.DisplayTextBoxesCAE
setLambda(double) - Method in class etomica.modules.adsorption.EOSSW
setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.modules.mu.P2SquareWellOneSide: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
setLambda(double) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
setLambda(double) - Method in class etomica.potential.P2DoubleWell: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.potential.P2PenetrableSquareWell: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.potential.P2SquareWell: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.potential.P2SquareWellRobust: Accessor method for well-diameter multiplier.
setLambda(double) - Method in class etomica.potential.P2TriangleWell
setLanguage(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the user language.
setLattice(FiniteLattice) - Method in class etomica.graphics.ColorSchemeCell
setLattice(FiniteLattice) - Method in class etomica.lattice.CellLattice.NeighborIterator
setLattice(SpaceLattice) - Method in class etomica.lattice.LatticeSum
setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLattice.Iterator
setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLatticeNbrIterator: Sets the lattice from which the iterates are given.
setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
setLattice(FiniteLattice) - Method in interface etomica.lattice.SiteIterator: Sets the lattice having the sites to be given by this iterator.
setLattice(CellLattice) - Method in class etomica.nbr.cell.ApiAACell
setLattice(CellLattice) - Method in class etomica.nbr.cell.molecule.MpiAACell
setLatticeBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
setLatticeBox(IBox) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
setLatticeConstant(double) - Method in interface etomica.lattice.CubicLattice: Sets the size of the unit cell, the length of each edge.
setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicBcc: The lattice constant is the size of the cubic primitive vectors of the lattice underlying this crystal.
setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicDiamond: The lattice constant is the size of the cubic primitive vectors of the lattice underlying this crystal.
setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicFcc: The lattice constant is the size of the cubic primitive vectors of the lattice underlying this crystal.
setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicSimple: The lattice constant is the size of the cubic primitive vectors.
setLatticeCorrec(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterRotPerturbMolecule
setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setLatticeEnergy(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
setLatticeEnergy(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDADB
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDirectSamplingTarget
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterOverlapSwitch
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterTargetTP
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkBennetHarmonic
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkBennetTarget
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetBennet
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetUmbrella
setLatticeEnergy(double) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
setLayers(int) - Method in class g3dsys.images.ImageShell: Sets the number of image shell layers to use
setLeafIndex(int) - Method in interface etomica.api.IAtom: Sets the atom's global index to the give value.
setLeafIndex(int) - Method in class etomica.atom.Atom
setLegend(DataTag[], String) - Method in class etomica.graphics.DisplayPlot
setLength(double) - Method in class etomica.math.geometry.LineSegment: Sets the length of the segment to the given value, keeping its orientation and the position of its midpoint fixed.
setLength(double) - Method in class etomica.models.hexane.CheckCBMCHexane
setLength(double) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
setLength(int) - Method in class org.jmol.util.StringXBuilder
setLengthAlkaneChain(int, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setLinPSpan(double) - Method in class etomica.normalmode.MeterDDP
setLinPSpan(double) - Method in class etomica.normalmode.MeterDP
setLiquidColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
setLiquidFilter(AtomFilter) - Method in class etomica.modules.droplet.P2Cohesion
setList(IAtomList) - Method in class etomica.atom.iterator.ApiIntraArrayList: Sets the list that will be used to generate the pairs.
setList(IAtomList) - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Sets the list for iteration.
setList(IMoleculeList) - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Sets the list for iteration.
setList(IMoleculeList) - Method in class etomica.atom.iterator.MpiIntraArrayList: Sets the list that will be used to generate the pairs.
setLnBias(int, double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
setLnBias(int, double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
setLocale(Locale) - Static method in class etomica.graph.view.rasterizer.Messages: Implements Localizable.setLocale(Locale).
setLocalVisitor(TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger: Replaces the current logger implementation by a new one.
setLogLevel(int) - Static method in class org.jmol.util.Logger: Activates all logging levels up through a given level.
setLongWall(int, boolean, boolean) - Method in class etomica.potential.P1HardBoundary
setLowerTorsLimit(double) - Method in class etomica.models.hexane.CheckCBMCHexane
setM(Matrix3f) - Method in class org.jmol.util.AxisAngle4f: Sets the value of this axis-angle to the rotational component of the passed matrix.
setM(Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the double value of the Matrix3f argument.
setM(Matrix4f) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to a copy of the passed matrix m1.
setM(Matrix3f) - Method in class org.jmol.util.Quaternion
setM3(Matrix3f) - Method in class org.jmol.util.Matrix4f: Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are initialized as if this were an identity matrix (ie, affine matrix with no translational component).
setMacrostateManager(MacrostateManager) - Method in class etomica.tmmc.IntegratorTMMC
setMakeLrc(boolean) - Method in class etomica.potential.P2SoftSphericalTruncated
setMakeReeHover(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to generate Ree-Hoover diagrams.
setMass(double) - Method in class etomica.chem.elements.ElementSimple: Sets mass of this element and updates reciprocal mass accordingly.
setMass(double) - Method in class etomica.potential.P1HardMovingBoundary
setMass(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs: Sets the mass; we assume the reduced mass is m/2 (correct for particles with identical mass).
setMass(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs: Sets the mass; we assume the reduced mass is m/2 (correct for particles with identical mass).
setMass(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
setMass(double) - Method in class etomica.units.systems.LJ
setMax(int) - Method in class etomica.lattice.IndexIteratorIncreasing: Sets a new maximum for iteration.
setMaxBlocks(int) - Method in class etomica.data.AccumulatorAverageCollapsing
setMaxBonds(int) - Method in class etomica.association.AssociationHelperBranched
setMaxBonds(int) - Method in class etomica.association.AssociationHelperMolecule
setmaxCosPhi(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
setmaxCosPhi(double) - Method in class etomica.association.BiasVolumeAceticAcid
setmaxCosTheta(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
setmaxCosTheta(double) - Method in class etomica.association.BiasVolumeAceticAcid
setMaxDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
setMaxDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
setMaxElement(int) - Method in class etomica.lattice.IndexIteratorTriangular: Sets the largest allow value for any element to have.
setMaxElement(int) - Method in class etomica.lattice.LatticeSum: Specifies the largest index element that will be included in the lattice sum.
setMaxElementMin(int) - Method in class etomica.lattice.IndexIteratorTriangular
setMaxHeight(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: If less than or equal to zero, the maximum height does not have any effect on the output image.
setMaximum(double) - Method in class etomica.graphics.DeviceSlider: Sets maximum value of slider; should be called after any calls to setPrecision.
setMaximum(double) - Method in class etomica.graphics.DeviceSpinner: Sets maximum value of slider
setMaximum(double) - Method in class etomica.graphics.DeviceThermoSlider: Set the maximum value for the temperature.
setMaximum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the maximum value for the temperature.
setMaximum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the maximum value for the N-Cell #.
setMaximum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the maximum value for the x- and y-Cell #.
setMaximum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the maximum value for the eigenvalue #.
setMaximum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the maximum value for the wavevector #.
setMaximumFractionDigits(int) - Method in class etomica.util.ScientificFormat
setMaximumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
setMaximumSeparation(double) - Method in class etomica.potential.P2Fene: Accessor method for harmonic energy parameter
setMaxIndex(int) - Method in class etomica.veos.HardRods
setMaxIndex(int) - Method in class etomica.veos.VanderWaals
setMaxInsertDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
setMaxInsertDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
setMaxIterations(int) - Method in class etomica.integrator.IntegratorRigidIterative
setMaxIterations(int) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
setMaxIterations(int) - Method in class etomica.integrator.IntegratorVelocityVerletShake
setMaxIterations(int) - Method in class etomica.modules.interfacial.FitTanh
setMaxIterations(int) - Method in class etomica.surfacetension.FitTanh
setMaxLatticeShell(int) - Method in class etomica.lattice.LatticeSumCrystal: Specifies the largest index element that will be included in the lattice sum.
setMaxLatticeShell(int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular: Specifies the largest index element that will be included in the lattice sum.
setMaxLatticeShell(int) - Method in class etomica.normalmode.HarmonicCrystal
setMaxLatticeShell(int) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
setMaxLatticeShell(int) - Method in class etomica.normalmode.NormalModesPotential
setMaxLatticeShell(int) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
setMaxLatticeShell(int) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
setMaxLatticeShell(int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol: Specifies the largest index element that will be included in the lattice sum.
setMaxLatticeShell(int) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
setMaxLength(int) - Method in class etomica.association.MCMoveAtomMonomer
setMaxLength(int) - Method in class etomica.association.MCMoveAtomSmer
setMaxLength(int) - Method in class etomica.association.MCMoveBiasUB
setMaxLength(int) - Method in class etomica.association.MCMoveRotateAssociated
setMaxNbrsVapor(int) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
setMaxPhi(double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
setMaxPhi(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
setMaxSample(double) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
setMaxSleep(int) - Method in class etomica.graphics.DeviceDelaySlider
setMaxSteps(long) - Method in class etomica.action.ActionIntegrate: Mutator method for the number of doStep steps to be performed by this integrator after it is started.
setMaxSteps(long) - Method in class etomica.action.activity.ActivityIntegrate: Mutator method for the number of doStep steps to be performed by this integrator after it is started.
setMaxWidth(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: If less than or equal to zero, the maximum width does not have any effect on the output image.
setMaxWidth(int) - Method in class etomica.util.ScientificFormat: the the maximum width of the decimal format.
setMCMove(MCMoveStepDependent) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
setMCMoveClusterTorsionMulti(MCMoveClusterTorsionMulti[]) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setMCMoveInsertDelete(MyMCMove, MyMCMove) - Method in class etomica.modules.adsorption.IntegratorHybrid
setMCMoves(MCMove[]) - Method in class etomica.integrator.mcmove.MCMoveManager: Sets moves in given array to be integrator's set of moves, deleting any existing moves.
setMDStepRepetitions(int) - Method in class etomica.modules.adsorption.IntegratorHybrid
setMDStepRepetitions(int) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
setMediaType(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the mediaType value.
setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setMembraneThickness(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setMembraneThicknessPerLayer(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setMeter(DataSourceScalar) - Method in class etomica.graphics.DisplayScrollingGraph: Specifies the meter that generates the displayed value.
setMeter(MeterNormalMode) - Method in class etomica.normalmode.WriteS
setMeter(IEtomicaDataSource) - Method in class etomica.virial.simulations.SimulationVirial
setMeter(MeterVirial, int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
setMeter(MeterVirial, int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
setMeter(int, MeterVirial) - Method in class etomica.virial.simulations.SimulationVirialPT
setMeterPotentialEnergy(DataSourceScalar) - Method in class etomica.integrator.IntegratorBox
setMeterTemperature(MeterTemperature) - Method in class etomica.integrator.IntegratorMD: Sets the temperature meter used to calculate temperature for velocity rescaling.
setMethanolParams(int) - Static method in class etomica.models.rowley.MethanolRouteParams
setMillerIndex(int, int) - Method in class etomica.lattice.LatticePlane: Sets the i-th Miller index to h, keeping the others fixed.
setMillerIndices(int[]) - Method in class etomica.lattice.LatticePlane: Sets the plane to the orientation specified by the given Miller indices applied to the current primitive.
setMinBondedAtomDistance(double) - Method in class etomica.association.AssociationHelperBranched
setMinBondedAtomDistance(double) - Method in class etomica.association.AssociationHelperDouble
setMinBondedMoleculeDistance(double) - Method in class etomica.association.AssociationHelperMolecule
setMinDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
setMinimum(double) - Method in class etomica.graphics.DeviceSlider: Sets minimum value of slider; should be called after any calls to setPrecision.
setMinimum(double) - Method in class etomica.graphics.DeviceSpinner: Sets minimum value of spinner
setMinimum(double) - Method in class etomica.graphics.DeviceThermoSlider: Set the minimum value for the temperature.
setMinimum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the minimum value for the temperature.
setMinimum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the minimum value for the N-Cell #.
setMinimum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the minimum value for the x- and y-Cell #.
setMinimum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the minimum value for the eigenvalue #.
setMinimum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the minimum value for the wavevector #.
setMinimumFractionDigits(int) - Method in class etomica.util.ScientificFormat
setMinimumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
setMinMax(int, int) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
setMinMu(double) - Method in class etomica.normalmode.DataSourceMuRoot1
setMinRadicalSites(int) - Method in class etomica.modules.catalysis.P2SquareWellSurface
setMobileSpecies(ISpecies) - Method in class etomica.config.GrainBoundaryTiltConfiguration
setModelSelectedSpecies(ModelSelectedSpecies) - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
setModelSpeciesSelection(ModelSpeciesSelection) - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
setModeNum(int[]) - Method in class etomica.normalmode.MCMoveHarmonic
setModes(int[]) - Method in class etomica.normalmode.MCMoveHarmonicStep: Sets the indices of the harmonic modes of the k=0 wave vector which should be sampled.
setModifier(ModifierBoolean) - Method in class etomica.action.ActionToggle: Specifies the boolean modifier that is set between true and false by the action.
setModifier(Modifier) - Method in class etomica.graphics.DeviceBox: Specifies the modifier that receives the edit.
setModifier(ModifierBoolean) - Method in class etomica.graphics.DeviceCheckBox: Returns the boolean modifier set by this button.
setModifier(Modifier) - Method in class etomica.graphics.DeviceNSelector
setModifier(Modifier) - Method in class etomica.graphics.DeviceSlider
setModifier(Modifier) - Method in class etomica.graphics.DeviceSpinner
setModifier(Modifier) - Method in class etomica.graphics.DeviceThermoSlider: Set the temperature modifier object.
setModifier(ModifierBoolean, String, String) - Method in class etomica.graphics.DeviceToggleButton
setModifier(ModifierBoolean) - Method in class etomica.graphics.DeviceToggleRadioButtons: Returns the boolean modifier set by this button.
setModifier(Modifier) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the temperature modifier object.
setModifier(Modifier) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the eigenvalue # modifier object.
setModifier(Modifier) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the wavevector # modifier object.
setMolecule(IMolecule, IMolecule) - Method in class etomica.action.WriteConfigurationP2DLPOLY
setMolecule(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorArrayList: Sets the first atom for iteration.
setMolecule(IMolecule) - Method in interface etomica.atom.iterator.MoleculeIteratorMoleculeDependent
setMolecule(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorSinglet: Defines atom returned by iterator and leaves iterator unset.
setMolecule(int, int) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
setMolecule(int, int) - Method in interface etomica.paracetamol.LatticeEnergyParacetamol
setMolecule(int, int) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.potential.PotentialCalculationTorqueSum
setMoleculeInfo(ISpecies, P2SemiclassicalMolecular.MoleculeInfo) - Method in class etomica.potential.P2SemiclassicalMolecular
setMoleculeListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setMoleculeListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setMoleculeListDisplayString(ArrayList<String>) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setMoleculeListDisplayTable(JTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setMoleculeListDisplayTable(JTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setMoleculeLists(IMoleculeList[]) - Method in class etomica.box.AtomSetAllMolecules
setMoleculeOffset(IVectorMutable) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setMoleculeOffset(IVectorMutable) - Method in class etomica.modules.sam.ConfigurationSAM
setMoleculePosition(IAtomPositionDefinition) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
setMolecules() - Method in class etomica.action.IntegratorDimerApproach
setMoleculeSource(MoleculeSource) - Method in class etomica.integrator.mcmove.MCMoveMolecule
setMoleculeSource(MoleculeSource) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange: Sets the AtomSource this class uses to pick molecules to delete.
setMoleculeSource(MoleculeSource) - Method in class etomica.models.hexane.MCMoveCBMC: Sets the AtomSource used to select molecules acted on by MC trials.
setMoleculeSource(MoleculeSource) - Method in class etomica.virial.MCMoveClusterAngleBend
setMoleculeSource(MoleculeSource) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
setMoment(double) - Method in class etomica.modules.vle.VLESim
setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setMomentOfInertia(double) - Method in class etomica.atom.AtomTypeOrientedSphere
setMomentOfInertia(IVector) - Method in class etomica.species.SpeciesSpheresRotatingMolecule: Sets the species' moment of inertia to the given moment.
setMomentSquare(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
setMonomerColor(Color) - Method in class etomica.association.ColorSchemeSmer: Sets the color used for all dimers.
setMonomerMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
setMovable(boolean) - Method in class etomica.graphics.DisplayCanvas
setMovable(boolean) - Method in class etomica.graphics.DisplayPolytope
setMovableAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerLJadatom
setMovableAtoms(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMadatom
setMovableAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCLJadatom
setMovableAtoms(double, IVectorMutable) - Method in class etomica.kmc.SimKMCMEAMadatom
setMovableAtomsCube(IVectorMutable, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMGB
setMovableAtomsList() - Method in class etomica.dimer.SimDimerMEAMGB
setMovableAtomsSphere(double, IVectorMutable) - Method in class etomica.dimer.SimDimerMEAMGB
setMove(MCMove) - Method in class etomica.data.DataSourceAcceptanceRatio: Sets the move for which the acceptance ratio is reported.
setMoveManager(MCMoveManager) - Method in class etomica.integrator.IntegratorManagerMC
setMoveManager(MCMoveManager) - Method in class etomica.integrator.IntegratorMC
setMu(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction: Sets a nominal bias for states that have not yet been visited.
setMu(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Mutator method for the chemical potential of the insertion/deletion species.
setMu(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
setMu(double, double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
setMu(double) - Method in class etomica.normalmode.DataSourceAvgPressure
setMu(double) - Method in class etomica.normalmode.DataSourceFEHistogram
setMu(double) - Method in class etomica.normalmode.DataSourceImposedFEFit
setMu(double) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
setMu(double) - Method in class etomica.normalmode.DataSourcePMu
setMV(Matrix3f, Vector3f) - Method in class org.jmol.util.Matrix4f: Initializes a Matrix4f from the rotation matrix and translation.
setN(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
setN(int) - Method in class etomica.potential.P4TorsionDreiding
setN(int) - Method in class etomica.veos.Ushcats
setName(String) - Method in class etomica.data.meter.MeterDihedralAngle
setName(String) - Method in class etomica.data.meter.MeterMomentumCOM
setName(String) - Method in class etomica.data.meter.MeterPositionCOM
setName(String) - Method in class etomica.data.meter.MeterPressureHardTensor
setName(String) - Method in class etomica.data.meter.MeterRDF
setName(String) - Method in class etomica.data.meter.MeterRDFPC
setName(String) - Method in class etomica.data.meter.MeterTensorVelocity
setName(String) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
setName(String) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
setName(String) - Method in class etomica.normalmode.MeterNormalMode
setName(String) - Method in class org.jmol.script.ScriptVariable
setNBins(int) - Method in class etomica.data.AccumulatorHistogram: Sets the number of bins in each histogram.
setNBins(int) - Method in interface etomica.util.Histogram: Sets the number of bins used by the Histogram.
setNBins(int) - Method in class etomica.util.HistogramDiscrete
setNBins(int) - Method in class etomica.util.HistogramExpanding: Sets the number of bins to n.
setNBins(int) - Method in class etomica.util.HistogramNotSoSimple
setNBins(int) - Method in class etomica.util.HistogramReweightedData
setNBins(int) - Method in class etomica.util.HistogramSimple
setNbrDistance(double) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
setNCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the n-Cell # modifier object.
setNCellNum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the current value for the N-Cell # slider/text box.
setNCellNum(int) - Method in class etomica.normalmode.NormalModes3D
setNCells(int[]) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
setNCells(int[]) - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
setNCellsX(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setNCellsX(int) - Method in class etomica.modules.sam.ConfigurationSAM
setNCellsZ(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setNCellsZ(int) - Method in class etomica.modules.sam.ConfigurationSAM
setNCrossLinkersAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
setNDiAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
setNDiol(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
setNegativePrefix(String) - Method in class etomica.util.ScientificFormat
setNegativeSuffix(String) - Method in class etomica.util.ScientificFormat
setNeighborDistance(double) - Method in class etomica.lattice.CellLattice.NeighborIterator: Defines neighbors to be all cells that are within the given distance from a central cell.
setNeighborRange(double) - Method in class etomica.nbr.CriterionPositionWall: Sets the neighbor range of the criterion.
setNeighborRange(double) - Method in class etomica.nbr.CriterionSimple
setNeighborRange(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
setNewWindowParametersForExport() - Method in class org.jmol.util.GData
setNextCriterion(IteratorDirective.PotentialCriterion) - Method in class etomica.atom.iterator.IteratorDirective.PotentialCriterion
setNGraft(int) - Method in class etomica.modules.colloid.ConfigurationColloid
setNInsert(int) - Method in class etomica.data.meter.MeterWidomInsertion: Number of Widom insertions attempted with each call to currentValue
setNInsert(int) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Number of Widom insertions attempted with each call to currentValue
setNInsert(int) - Method in class etomica.liquidLJ.MeterWidomInsertionP: Number of Widom insertions attempted with each call to currentValue
setNMajor(int) - Method in class etomica.graphics.DeviceSlider
setNMaxReweight(int) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
setNMinor(int) - Method in class etomica.graphics.DeviceSlider
setNMolecules(ISpecies, int) - Method in interface etomica.api.IBox: Sets the number of molecules in this box of the given ISpecies to n.
setNMolecules(ISpecies, int) - Method in class etomica.box.Box
setNMonoAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
setNMonoOl(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
setNo72B2B3NonAdd(boolean) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
setNoisyAdjustment(boolean) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D: used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to assign a noisy shade to the surface it will render
setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.util.GData
setNominalFluctuation(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
setNominalReference(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setNominalTheta(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
setNominalTheta(double) - Method in class etomica.normalmode.MeterThetaDeviation
setNoOfSpheres(JTextField) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
setNoOfSteps(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setNoOfSteps(int) - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
setNormalModes(NormalModes) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
setNormalModes(NormalModes) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
setNormalPoint(IVector, IVector) - Method in class etomica.math.geometry.Plane: Defines the plane via a normal vector (1st argument) and a point (2nd argument).
setNormalVector(IVector) - Method in class etomica.math.geometry.Plane: Sets the orientation of the plane to be normal to the given vector.
setNPoints(int) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
setnPoints(int[]) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setnReactCO(int) - Method in class etomica.modules.catalysis.ReactionManagerCO
setNRows(int) - Method in class etomica.data.types.DataTable.DataInfoTableFactory: Sets the number of rows.
setNSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the post slider value changed action.
setNSpheres(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setNSpheres(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setNthSpeciesAdded(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
setNthSpeciesSelectedIndex(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setNTicks(int) - Method in class etomica.graphics.DisplayScrollingGraph
setNullPotential(PotentialHard) - Method in class etomica.integrator.IntegratorHard.Agent
setNullPotential(PotentialHard, IAtomType) - Method in class etomica.integrator.IntegratorHard: Sets the "null" potential for the given AtomType.
setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHe
setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
setNumAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setNumAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setNumAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
setNumAlpha(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
setNumAlpha(int) - Method in class etomica.normalmode.MeterOverlapSwitch
setNumAlpha(int) - Method in class etomica.normalmode.MeterTargetTP
setNumAlpha(int) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
setNumAlpha(int) - Method in class etomica.overlap.MeterOverlap
setNumAlpha(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
setNumAlpha(int) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
setNumAlpha(int) - Method in class etomica.virial.simulations.SimulationVirialOverlap: Sets the number of alpha values used for the production stage of the simulation
setNumAlpha(int) - Method in class etomica.virial.simulations.SimulationVirialOverlap2: Sets the number of alpha values used for the production stage of the simulation.
setNumAtoms(int) - Method in class etomica.chem.models.ModelChain: Sets the number of atoms per chain molecule.
setNumBeads(int) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
setNumber(double) - Method in class etomica.modules.materialfracture.StrainColorScheme
setNumberFraction(double[]) - Method in class etomica.species.SpeciesSpheresHetero: Sets the number fraction of each child atom type made by this factory.
setNumberOfModesChanged(int) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setNumberOfTrials(int) - Method in class etomica.models.hexane.MCMoveCBMC
setNumBoxes(int) - Method in class etomica.integrator.IntegratorPT.BoxTracker: Specifies the number of boxes that are tracked.
setNumCells(int) - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
setNumCO(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setNumCollapseBins(int) - Method in class etomica.util.HistoryCollapsing: Sets the number of "collapse" bins.
setNumDigitColumns(int) - Method in class etomica.graphics.DisplayTable
setNumEquilibrationSubsteps(int) - Method in class etomica.thermointegration.IntegratorThermodynamic: Sets the number of steps equilibration steps performed at each thermodynamic state point before data collection begins.
setNumerator(int) - Method in interface etomica.graph.model.Coefficient
setNumerator(int) - Method in class etomica.graph.model.impl.CoefficientImpl
setNumFactors(int) - Method in interface etomica.graph.model.Graph
setNumFactors(int) - Method in class etomica.graph.model.impl.GraphImpl
setNumGraft(int) - Method in class etomica.modules.colloid.ColloidSim
setNumLeafAtoms(int) - Method in class etomica.species.SpeciesSpheres: Specifies the number of child atoms in each atom constructed by this factory.
setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setNumO2(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setNumP(int) - Method in class etomica.normalmode.MeterDDP
setNumP(int) - Method in class etomica.normalmode.MeterDP
setNumRawDataDoubles(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog: Sets the number of times the random block generation method is used.
setNumSubSteps(long) - Method in class etomica.overlap.IntegratorOverlap: Sets the number of total number of integrator steps the sub-integrators perform for every step of the overlap integrator.
setNumSubsteps(int) - Method in class etomica.thermointegration.IntegratorThermodynamic: Sets the number of steps performed at each thermodynamic state point.
setNumSubSteps(int) - Method in class etomica.virial.overlap.IntegratorOverlap: Sets the number of total number of integrator steps the sub-integrators perform for every step of the overlap integrator.
setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBonding
setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
setNumThreads(int, IBox) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
setNumThreads(int, IBox) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingRegrow: Sets the number of configurational bias trials
setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange: Sets the number of configurational bias trials
setNumXCells(int) - Method in class etomica.modules.sam.Sam
setNumZCells(int) - Method in class etomica.modules.sam.Sam
setNValues(int) - Method in class etomica.data.DataSourceUniform: Sets the number of uniformly spaced values.
setOelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
setOffset(IVector) - Method in class etomica.config.ConformationChainLinear
setOffset(IVector) - Method in class etomica.config.ConformationLinear
setOffset(IVectorMutable) - Method in class etomica.modules.sam.P1Sinusoidal
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
setOmegaSquared(double[][], double[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setOmegaSquared(double[][], double[]) - Method in class etomica.normalmode.IntegratorHarmonic
setOmegaSquared(double[][]) - Method in class etomica.normalmode.MCMoveHarmonic
setOmegaSquared(double[][], double[]) - Method in class etomica.normalmode.MCMoveSingleMode
setOmegaSquared(double[][]) - Method in class etomica.normalmode.MeterHarmonicEnergy
setOmegaSquared(double[][]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
setOneEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the "eigenvalues" button to its selected state.
setOneEVal(boolean) - Method in class etomica.normalmode.IntegratorHarmonic
setOneEValButtonsVisibility(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
setOneWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the "wave vector" button to its selected state.
setOneWV(boolean) - Method in class etomica.normalmode.IntegratorHarmonic
setOneWVButtonsVisibility(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
setOnlyConnected(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to only generate clusters that are singly-connected.
setOnlyDoublyConnected(boolean) - Method in class etomica.virial.cluster.ClusterGenerator: Set whether to only generate clusters that are doubly-connected.
setOrderBeta(int) - Method in class etomica.virial.cluster.VirialDiagramsPT
setOrientation(IMolecule, IOrientationFull3D) - Method in interface etomica.atom.OrientationCalc: Sets the orientation of the given molecule to be equal to the given orientation.
setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.atom.OrientationCalcAtom
setOrientation(IMolecule, double[]) - Method in interface etomica.atom.OrientationCalcQuaternion
setOrientation(IVector) - Method in class etomica.config.ConformationChainLinear
setOrientation(IVector) - Method in class etomica.config.ConformationLinear
setOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater3P
setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater3P
setOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater4P
setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater4P
setOrientation(IOrientationFull3D) - Method in class etomica.space3d.RotationTensor3D
setOrientationCalc(ISpecies, OrientationCalc) - Method in class etomica.integrator.IntegratorRigidIterative
setOrientationCalc(ISpecies, OrientationCalc) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
setOrientationCalc(ISpecies, OrientationCalcQuaternion) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
setOrientations(IVector[][], double[], CoordinateDefinitionHSDimer.IntegerFunction) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
setOrientationSites(IAtomTypeOriented, DisplayBoxCanvasG3DSys.OrientedSite[]) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
setOrientationVectorAlpha(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setOrientationVectorAlpha(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setOrientationVectorBeta(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setOrientationVectorBetaInitial(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setOrientationVectorBetaLatticeSum(ISpace, double, double[][]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setOrientationVectorGamma(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setOrientationVectorGamma(ISpace) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setOrigin(IVector) - Method in class etomica.lattice.LatticePlane: Sets the origin from which the position of the atom is measured.
setOriginShift(int, int) - Method in class etomica.graphics.DisplayBox: Amount (in pixels) of a simple shift (translation) applied in determing origin.
setOrtho(boolean, boolean) - Method in class etomica.dimer.IntegratorDimerRT: Set's the Dimer search's orthogonality criteria.
setOtherAngles(double[]) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setOtherDensities(double[]) - Method in class etomica.normalmode.MeterDDP
setOtherDensities(double[]) - Method in class etomica.normalmode.MeterDP
setOtherSwitchFrac(double[]) - Method in class etomica.normalmode.MeterOverlapSwitch
setOtherTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
setOtherTemperatures(double[]) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setOtherTemperatures(double[]) - Method in class etomica.normalmode.MeterTargetTP
setOut(PrintStream) - Method in class etomica.data.DataSinkConsole: Sets the output print stream where data is written.
setOuterGraph(Graph) - Method in class etomica.graph.iterators.CartesianIterator
setOuterIterator(GraphIterator) - Method in class etomica.graph.iterators.CartesianIterator
setOuterList(IAtomList) - Method in class etomica.atom.iterator.ApiInterArrayList: Sets the list that will be used to generate the pairs.
setOuterList(IMoleculeList) - Method in class etomica.atom.iterator.MpiInterArrayList: Sets the list that will be used to generate the pairs.
setOuterPermutation(byte[]) - Method in class etomica.graph.iterators.CartesianPermutator
setOuterPermutator(DefaultPermutator) - Method in class etomica.graph.iterators.CartesianPermutator
setOverlapSplitter(DataSplitter) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
setOverwrite(boolean) - Method in class etomica.normalmode.WriteS
setPaddingSigma(double) - Method in class etomica.graphics.DisplayBox: Sets the amount of padding added around the edge of the drawing area.
setPaintInterval(IBox, int) - Method in class etomica.graphics.SimulationGraphic: setPaintInterval() Sets the integrator interval between repaint actions to the value specified for the given Box.
setParameter(String, String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
setParameterLimits(String, double, double) - Method in class etomica.graphics.DevicePlotPoints: Sets the minimum and maximum allowable values for a function parameter.
setParameters(IAtomType, ParameterSetMEAM) - Method in class etomica.meam.PotentialMEAM
setParameters(String) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
setParameters(double) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
setParameters(String) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
setParameters(double) - Method in class etomica.yukawa.P2HC2Yukawa: Parameter calculation method.
setParametersIMC(IAtomType, ParameterSetMEAM) - Method in class etomica.meam.PotentialMEAM
setParameterWrapper(ParameterBase) - Method in class etomica.util.ParseArgs: Sets the parameterWrapper
setParameterWrapper(ParameterBase) - Method in class etomica.util.ReadParameters: Sets the parameterWrapper
setParameterWrapper(ParameterBase) - Method in class etomica.util.WriteParameters: Sets the parameterWrapper
setParams() - Method in class etomica.virial.BnJHBVArgon_Analytic
setParent(IMolecule) - Method in interface etomica.api.IAtom: Informs the Atom that the given AtomGroup is its parent.
setParent(IMolecule) - Method in class etomica.atom.Atom: Informs the Atom that the given AtomGroup is its parent.
setParseIntegerOnly(boolean) - Method in class etomica.util.ScientificFormat
setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
setPass2(boolean) - Method in class org.jmol.util.GData
setPauseAfterEachAction(boolean) - Method in class etomica.action.activity.ActivityGroupSeries
setPbcEnforcer(BoxImposePbc) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
setPbcEnforcer(BoxImposePbc) - Method in class etomica.nbr.list.NeighborListManager
setPCenter(double[]) - Method in class etomica.normalmode.MeterDDP
setPCenter(double[]) - Method in class etomica.normalmode.MeterDP
setPcom(double[]) - Method in class etomica.util.numerical.Function1d
setPeriodicity(boolean[]) - Method in class etomica.lattice.RectangularLatticeNbrIterator
setPerpendicularTo(IVector) - Method in class etomica.space3d.Vector3D
setPerspectiveDepth(boolean) - Method in class g3dsys.control.G3DSys
setPHarmonic(double, double) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
setPhi(double) - Method in class etomica.models.hexane.CheckCBMCHexane
setPhi(double) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
setPhi(double) - Method in class etomica.potential.P4TorsionDreiding
setPhongExponent(int) - Static method in class org.jmol.util.GData: p in I = df * (N dot L) + sf * (R dot V)^p
setPistonPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.BoundaryPistonCylinder
setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayBox: Sets unit for conversion between simulation units and display pixels.
setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayCanvas: Sets unit for conversion between simulation units and display pixels.
setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayPolytope: Sets unit for conversion between simulation units and display pixels.
setPixelUnitToMillimeter(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the millimeters per pixel constant.
setPlaneColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Sets the color of the plane.
setPlayDumb(boolean) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction: With "play dumb" on, the bias will simply try to produce a flat histogram based on previously-measured free energy differences (no fitting or defect free energy will be used).
setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
setPolytope(Polytope) - Method in class etomica.graphics.DisplayPolytope: Specifies the polytope for this display.
setPolytopeCanvas(DisplayCanvas) - Method in class etomica.graphics.DisplayPolytope
setPoreCenters(IVectorMutable[]) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
setPoreDim(int) - Method in class etomica.space.BoundaryRectangularPore: Sets the periodic dimension to that indicated by the given value (0 is x-dimension, 1 is y-dimension, etc.).
setPoreRadius(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
setPosition(IAtom, String) - Method in class etomica.config.ConfigurationFile
setPosition(IAtom, String) - Method in class etomica.config.ConfigurationOrientedFile
setPosition(double) - Method in class etomica.lattice.LatticePlane: Sets to the position of the i-th plane from the one through the origin.
setPosition(IVector) - Method in class etomica.math.geometry.Hypersphere
setPosition(IVector) - Method in class etomica.math.geometry.Polytope: Sets the position of the geometric center of the polytope.
setPosition(IVector) - Method in interface etomica.math.geometry.Shape: Sets the position of the shape, which typically represents some central point within it.
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.action.BoxImposePbc
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.atom.AtomFilterInShape: Sets position definition.
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.data.meter.MeterProfileByAtoms
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.data.meter.MeterProfileByVolume
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
setPositionDefinition(IAtomPositionDefinition) - Method in class etomica.virial.CoordinatePairMoleculeSet
setPositionSource(RandomPositionSource) - Method in class etomica.data.meter.MeterProfile: Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) - Method in class etomica.data.meter.MeterWidomInsertion: Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete: Sets a new RandomPositionSource for this move to use.
setPositionSource(RandomPositionSource) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange: Sets a new RandomPositionSource for this move to use.
setPositionSource(RandomPositionSource) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) - Method in class etomica.liquidLJ.MeterWidomInsertionP: Sets a new RandomPositionSource for this meter to use.
setPositionSource(RandomPositionSource) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
setPositivePrefix(String) - Method in class etomica.util.ScientificFormat
setPositiveSuffix(String) - Method in class etomica.util.ScientificFormat
setPostAction(IAction) - Method in class etomica.graphics.Device: Sets an action to be performed after the primary action executed by the device.
setPotential(DataSourceScalar) - Method in class etomica.data.meter.MeterEnergy
setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
setPotential(String) - Method in class etomica.modules.insertion.InsertionGraphic
setPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
setPotential(String) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
setPotential(String) - Method in class etomica.modules.swmd.SwmdGraphic
setPotential(IPotentialAtomic[]) - Method in class etomica.normalmode.MCMoveAtomCoupled
setPotential(IPotentialAtomic) - Method in class etomica.normalmode.MCMoveAtomCoupled
setPotential(Potential2) - Method in class etomica.normalmode.MCMoveAtomSuperBox
setPotential(IPotentialMolecular) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
setPotential(Potential2SoftSpherical) - Method in class etomica.normalmode.NormalModesPotential
setPotential(Potential2SoftSpherical) - Method in class etomica.normalmode.NormalModesSoftSpherical
setPotential(PotentialGroup) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
setPotentialCalculation(PotentialCalculationEnergySum) - Method in class etomica.data.meter.MeterPotentialEnergy
setPotentialCollectionFactory(ICollectionPotential) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
setPotentialGroupInterNonBondedLike(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setPotentialGroupInterNonBondedUnlike(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
setPotentialGroupIntraBonded(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setPotentialIntraBondedTorsion(IPotentialAtomic) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setPotentialJList(JList) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialJList(JList) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialList(Class[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setPotentialListAtoms() - Method in class etomica.dimer.SimDimerMEAMadatom
setPotentialListAtoms() - Method in class etomica.kmc.SimKMCMEAMadatom
setPotentialListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialMaster(IPotentialMaster) - Method in class etomica.data.meter.MeterHyperVirial
setPotentialMaster(IPotentialMaster) - Method in class etomica.data.meter.MeterPressure
setPotentialMaster(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPU
setPotentialMaster(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCut
setPotentialMaster(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCutLS
setPotentialMaster(IPotentialMaster) - Method in class etomica.modules.vle.MeterPressure2: Sets the integrator associated with this instance.
setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.BoxAgentSourceCellManagerList
setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.NeighborCellManagerList
setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
setPotentialMaster(IPotentialMaster) - Method in class etomica.nbr.PotentialGroupHybrid
setPotentialMaster(IPotentialMaster) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
setPotentialMaster(PotentialMasterList, IAtomType[]) - Method in class etomica.potential.P2SquareWellRobust: Informs the square-well class what the potential master is (if neighbor listing is used) and the types of atoms interacting with this potential.
setPotentialMaster(IPotentialMaster) - Method in class etomica.potential.PotentialGroup
setPotentialMaster(IPotentialMaster) - Method in class etomica.virial.ClusterSumExternalField
setPotentialMasterDADv2(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCut
setPotentialMasterDADv2(IPotentialMaster) - Method in class etomica.liquidLJ.MeterPUCutLS
setPotentialMasterDADv2(IPotentialMaster, double[]) - Method in class etomica.normalmode.MeterSolidDACut
setPotentialMC(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
setPotentialMolecularNonBondedLike(IPotentialMolecular) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
setPotentialMolecularUnlike(IPotentialMolecular) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
setPotentialParamAndValuesString(String[][]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setPotentialParamDispayTable(JTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialParamDispayTable(JTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialParamDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialParamDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialParamDisplayTM(ModelPotParamDisplayTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialParamDisplayTM(ModelPotParamDisplayTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setPotentialParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setPotentialParamString(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setPotentialPseudo(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
setPotentialRange(double) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular: Sets the potential range to the given value.
setPotentialRange(double) - Method in class etomica.nbr.cell.NeighborCellManager: Sets the potential range to the given value.
setPotentialsClassList(Class[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setPotentialsCollectionBuilder(BuilderCollectionPotential) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
setPotentialSites(String[]) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setPotentialsSelectedIndex(int[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setPotentialsSelectedIndex(int, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setPreAction(IAction) - Method in class etomica.graphics.Device: Sets an action to be performed before the primary action executed by the device.
setPrecision(int) - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
setPrecision(int) - Method in class etomica.graphics.DecimalSlider: Mutator method for precision of slider.
setPrecision(int) - Method in class etomica.graphics.DeviceBox: Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) - Method in class etomica.graphics.DeviceSlider
setPrecision(int) - Method in class etomica.graphics.DeviceTernarySelector: Mutatator method for the precision of the mole fractions.
setPrecision(int) - Method in class etomica.graphics.DeviceThermoSlider: Set the precision of the scrollbar.
setPrecision(int) - Method in class etomica.graphics.DisplayTable: Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) - Method in class etomica.graphics.DisplayTextBox: Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) - Method in class etomica.graphics.DisplayTextBoxesCAE: Accessor method of the precision, which specifies the number of significant figures to be displayed.
setPrecision(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the precision of the scrollbar.
setPrecision(int) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
setPrecisionLimit(int) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
setPrefactor(double) - Method in class etomica.virial.cluster.ClusterDiagramTree
setPreferredSize(int, int) - Method in class etomica.graphics.DeviceTable: Set the preferred size attribute of the scrolled window the table sits on.
setPrefix(Prefix) - Method in class etomica.units.PrefixedUnit: Changes prefix to given instance if prefixAllowed flag is true
setPRes(double) - Method in class etomica.normalmode.MeterSolidDA
setPressure(double) - Method in class etomica.association.MCMoveVolumeAssociated
setPressure(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
setPressure(double) - Method in class etomica.data.meter.MeterWidomInsertion
setPressure(double) - Method in class etomica.integrator.mcmove.MCMoveVolume
setPressure(double, double, IFunction) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
setPressure(double) - Method in class etomica.liquidLJ.MeterWidomInsertionP
setPressure(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
setPressure(double) - Method in class etomica.modules.adsorption.DataSourceDensityFunction
setPressure(double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeSolid
setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
setPressure(double) - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
setPressure(double) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
setPressure(double) - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
setPressure(double) - Method in class etomica.potential.P1HardMovingBoundary
setPrevX(float) - Method in class etomica.graphics.DisplayCanvas
setPrevY(float) - Method in class etomica.graphics.DisplayCanvas
setPrimitive(Primitive) - Method in class etomica.lattice.BravaisLattice: Sets the primitive for this lattice to the one given, and updates the site positions.
setPrimitive(Primitive) - Method in class etomica.lattice.LatticePlane
setPrimitive(Primitive) - Method in class etomica.normalmode.NormalModesSoftSpherical
setProfileDim(int) - Method in class etomica.data.meter.MeterProfile: Accessor method for vector describing the direction along which the profile is measured.
setProfileDim(int) - Method in class etomica.data.meter.MeterProfileByAtoms: Accessor method for vector describing the direction along which the profile is measured.
setProfileDim(int) - Method in class etomica.data.meter.MeterProfileByVolume: Accessor method for vector describing the direction along which the profile is measured.
setProfileDim(int) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
setProperty(String, String) - Method in interface etomica.graph.engine.Environment
setProperty(String, String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
setProperty(String) - Method in class etomica.graphics.DeviceSlider
setProperty(String) - Method in class etomica.graphics.DeviceSpinner
SetPropertyFilter - Class in etomica.graph.operations
SetPropertyFilter(Property) - Constructor for class etomica.graph.operations.SetPropertyFilter
setPT2(boolean) - Static method in class etomica.potential.P2O2Bartolomei
setPullFactor(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
setPushInterval(long) - Method in class etomica.data.DataAccumulator: Accumulated data are pushed to the data sinks after every pushInterval calls to putData.
setQ(double) - Method in class etomica.chem.electrostatics.Charge
setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P22CLJQ
setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P2LJQ
setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P2LJQQ
setQuality(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the JPEG encoding quality.
setQuaternions(double[]) - Method in class etomica.space3d.RotationTensor3D
setQuiet(boolean) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Sets the quiet flag, indicating if unsafe-neighbor conditions should generate an error message (would not want this if atoms were inserted in a MC move, for example).
setQuiet(boolean) - Method in class etomica.nbr.list.NeighborListManager: Sets the quiet flag, indicating if unsafe-neighbor conditions should generate an error message (would not want this if atoms were inserted in a MC move, for example).
setQuiet(boolean) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
setQuiet(boolean) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
setQuiet(boolean) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
setR0(double) - Method in class etomica.potential.P2Harmonic: Sets the the separation at which potential is at its minimum.
setR2Cut(double) - Method in class etomica.data.meter.MeterBondOrderParameterQ
setr2d2udr2(double[]) - Method in class etomica.virial.PercusYevick1QC
setRadicalColor(IAtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
setRadioGroupPostAction(IAction) - Method in class etomica.graphics.DeviceThermoSlider: Sets an action to be performed after a isothermal/adiabatic button is pressed and the integrator's isothermality has been set.
setRadius(double) - Method in class etomica.math.geometry.Hypersphere
setRadius(double) - Method in class etomica.potential.P1SoftBoundary: Sets the radius.
setRandom(IRandom) - Method in class etomica.simulation.Simulation: Set the simulation's random number generator to the given one.
setRandom(IRandom) - Method in class etomica.virial.cluster.ClusterDiagramTree
setRandomCube(IRandom) - Method in interface etomica.space.IVectorRandom: Assigns each component to (its own) random value between -0.5 and + 0.5.
setRandomCube(IRandom) - Method in class etomica.space1d.Vector1D
setRandomCube(IRandom) - Method in class etomica.space2d.Vector2D
setRandomCube(IRandom) - Method in class etomica.space3d.Vector3D
setRandomCube(IRandom) - Method in class etomica.spaceNd.VectorND
setRandomInSphere(IRandom) - Method in interface etomica.space.IVectorRandom: Assigns this vector to equal a point chosen randomly in the volume of a unit spheres.
setRandomInSphere(IRandom) - Method in class etomica.space1d.Vector1D
setRandomInSphere(IRandom) - Method in class etomica.space2d.Vector2D
setRandomInSphere(IRandom) - Method in class etomica.space3d.Vector3D
setRandomInSphere(IRandom) - Method in class etomica.spaceNd.VectorND
setRandomNumberGenerator(IRandom) - Method in class etomica.association.AtomSourceRandomDimer
setRandomNumberGenerator(IRandom) - Method in class etomica.association.AtomSourceRandomSmer
setRandomNumberGenerator(IRandom) - Method in class etomica.association.MoleculeSourceRandomDimer
setRandomNumberGenerator(IRandom) - Method in class etomica.atom.AtomSourceRandomLeaf: Sets the random number generator used to pick atoms
setRandomNumberGenerator(IRandom) - Method in class etomica.atom.AtomSourceRandomSpecies: Sets the random number generator used to pick atoms
setRandomNumberGenerator(IRandom) - Method in class etomica.atom.MoleculeSourceRandomMolecule: Sets the random number generator used to pick molecules
setRandomSphere(IRandom) - Method in interface etomica.space.IVectorRandom: Assigns this vector to equal a point chosen randomly on the surface of a unit sphere.
setRandomSphere(IRandom) - Method in class etomica.space1d.Vector1D
setRandomSphere(IRandom) - Method in class etomica.space2d.Vector2D
setRandomSphere(IRandom) - Method in class etomica.space3d.Vector3D: Creating a random unit vector on unit sphere Uses only two random number generator at a time Based on M.P.
setRandomSphere(IRandom) - Method in class etomica.spaceNd.VectorND: Creating a random unit vector on unit sphere Uses only two random number generator at a time Based on M.P.
setRange(int[]) - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare: Sets the range used to define the neighboring sites.
setRange(double, double) - Method in class etomica.meam.PotentialCuLREP
setRange(double) - Method in class etomica.meam.PotentialEFS
setRange(double) - Method in class etomica.meam.PotentialFeEAM
setRange(double) - Method in class etomica.meam.PotentialFeEAM_LS
setRange(double) - Method in class etomica.models.nitrogen.P2Nitrogen
setRange(int, double, double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
setRange(double, double) - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
setRange(double) - Method in class etomica.modules.adsorption.P1Wall
setRange(double) - Method in class etomica.modules.colloid.P1Wall
setRange(double) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
setRange(double) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
setRange(double) - Method in class etomica.nbr.cell.PotentialMasterCell
setRange(double) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Sets the interaction range, which affects the cell-list neighbor iteration used to generate candidate neighbors for neighbor listing.
setRange(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
setRange(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Sets the range that determines how far to look for neighbors.
setRange(double) - Method in class etomica.nbr.list.NeighborListManager: Sets the interaction range, which affects the cell-list neighbor iteration used to generate candidate neighbors for neighbor listing.
setRange(double) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
setRange(double) - Method in class etomica.nbr.list.PotentialMasterList: Sets the range that determines how far to look for neighbors.
setRange(double) - Method in class etomica.nbr.PotentialMasterHybrid
setRange(double) - Method in class etomica.potential.P2ReactionFieldDipole
setRange(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
setRatio(double, double) - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
setRawData(AccumulatorAverageBlockless.AllData) - Method in class etomica.data.AccumulatorAverageBlockless
setRawData(AccumulatorAverageBlockless.AllData) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
setRCut(double) - Method in class etomica.potential.EwaldSummation: Sets a new value of rCutRealES This will not alter values of alpha or nRealShells!
setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibody
setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
setrdfdr(double[]) - Method in class etomica.virial.HypernettedChain
setrdfdr(double[]) - Method in class etomica.virial.PercusYevick
setrdudr(double[]) - Method in class etomica.virial.PercusYevick1QC
setRe(double) - Method in class etomica.potential.P2ModifiedMorse
setRe(double) - Method in class etomica.potential.P2Morse
setReader(ConsoleReader) - Method in interface etomica.graph.engine.Console
setReader(ConsoleReader) - Method in class etomica.graph.engine.ConsoleUI
setRef(Quaternion) - Method in class org.jmol.util.Quaternion
setRefAvg(DataOverlap.DataSourceOverlapAvg) - Method in class etomica.overlap.DataOverlap
setReferenceDataInterval(int) - Method in class etomica.normalmode.SimOverlapModule
setReferenceFracSource(IntegratorOverlap.ReferenceFracSource) - Method in class etomica.overlap.IntegratorOverlap: Sets the DataSource that retrieves data from both boxes and provides information to the integrator about their progress, which is used to decide how much to sample each system.
setReflecting(boolean[]) - Method in class etomica.lattice.IndexIteratorReflecting: Indicates the indexes of the elements that are subject to reflection.
setRefPref(double, double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
setRefPref(double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
setRefPref(double, double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
setRefPref(double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
setRefPref(double, double) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
setRefPref(double, double) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
setRefPref(double) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
setRefPref(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
setRefPref(double) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
setRefPref(double) - Method in class etomica.normalmode.MeterSamplingHarmonic
setRefPref(double) - Method in class etomica.normalmode.MeterSamplingTarget
setRefPref(double) - Method in class etomica.normalmode.MeterWorkBennetHarmonic
setRefPref(double) - Method in class etomica.normalmode.MeterWorkBennetTarget
setRefPref(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
setRefPref(double) - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
setRefPref(double) - Method in class etomica.normalmode.MeterWorkTargetBennet
setRefPref(double) - Method in class etomica.normalmode.MeterWorkTargetUmbrella
setRefPref(double) - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
setRefPref(double) - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
setRefPref(double) - Method in class etomica.normalmode.SimBennet
setRefPref(double) - Method in class etomica.normalmode.SimHarmonicUmbrella
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlap
setRefPref(double) - Method in class etomica.normalmode.SimOverlap
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapLJ
setRefPref(double) - Method in class etomica.normalmode.SimOverlapLJ
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphere
setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphere
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSSnxy
setRefPref(double) - Method in class etomica.normalmode.SimOverlapSSnxy
setRefPref(double) - Method in class etomica.normalmode.SimTargetUmbrella
setRefPref(double) - Method in class etomica.normalmode.SimUmbrella
setRefPref(double) - Method in class etomica.normalmode.SimUmbrellaSoftSphere
setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setRefStepFraction(double) - Method in class etomica.overlap.IntegratorOverlap
setRejectable(boolean) - Method in class etomica.normalmode.MCMoveHarmonic
setRelaxAction(MoleculeAction) - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
setRelaxAction(MoleculeAction) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
setRelaxationRateH(double) - Method in class etomica.integrator.IntegratorGear4NPH
setRelaxationRateP(double) - Method in class etomica.integrator.IntegratorGear4NPH
setRemove(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setRemoveSpecies1(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setRemoveSpecies2(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setRemoveSpecies3(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setRemoveSpeciesAfterAlertFlag(boolean) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setRepaintInterval(int) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
setRepaintSleep(int) - Method in class etomica.graphics.SimulationGraphic
setRepeatCurrentAction(boolean) - Method in class etomica.action.activity.Controller: Flag indicating whether the current action should be repeated indefinitely before moving on to the next action.
setRescalingToFitVolume(boolean) - Method in class etomica.config.ConfigurationLattice: Sets the resizeLatticeToFitVolume flag, which if true indicates that the primitive vectors should be resized to fit the dimensions of the box.
setRescalingToFitVolume(boolean) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice: Sets the resizeLatticeToFitVolume flag, which if true indicates that the primitive vectors should be resized to fit the dimensions of the box.
setRescalingToFitVolume(boolean) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice: Sets the resizeLatticeToFitVolume flag, which if true indicates that the primitive vectors should be resized to fit the dimensions of the box.
setReservoirSize(int) - Method in class etomica.atom.AtomLeafAgentManager: Sets the size of the manager's "reservoir".
setReservoirSize(int) - Method in class etomica.atom.MoleculeAgentManager: Sets the size of the manager's "reservoir".
setReset(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setReset(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setResetAction(IAction) - Method in class etomica.graphics.DeviceNSelector
setResidual(boolean) - Method in class etomica.data.meter.MeterWidomInsertion: Sets flag specifying if full or residual chemical potential is computed Default is true (only residual is computed)
setResidual(boolean) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
setResizable(boolean) - Method in class etomica.graphics.DisplayCanvas
setResizable(boolean) - Method in class etomica.graphics.DisplayPolytope
setResizeOnNewBox(boolean) - Method in class etomica.graphics.DisplayBox: Set the flag indicating whether the graphic should resize from its currently displayed size when a new box is set.
setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
setRm(double) - Method in class etomica.potential.P2Exp6Buckingham
setRmax(double) - Method in class etomica.data.meter.MeterDihedralAngle
setRmax(double) - Method in class etomica.potential.P2Exp6Buckingham
setRmSquared(double) - Method in class etomica.potential.P2Exp6Buckingham
setRotationAxis(IVector, double) - Method in class etomica.space3d.RotationTensor3D: Sets the tensor for rotation about the axis v by an angle theta.
setRotationAxisCT(IVector, double) - Method in class etomica.space3d.RotationTensor3D
setRotationBOTTOM(int, double) - Method in class etomica.config.GrainBoundaryTiltConfiguration
setRotationMatrix(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
setRotationScale(Matrix3f) - Method in class org.jmol.util.Matrix4f: Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.
setRotationTOP(int, double) - Method in class etomica.config.GrainBoundaryTiltConfiguration: Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by the given angle.
setRotNum(int) - Method in class etomica.dimer.IntegratorDimerRT
setRoute(int) - Method in class etomica.action.IntegratorDimerApproach
setRoute(boolean) - Method in class etomica.virial.HypernettedChain
setRoute(boolean) - Method in class etomica.virial.PercusYevick
setRouteParams(double[][]) - Method in class etomica.action.IntegratorDimerApproach
setRow(int, float, float, float) - Method in class org.jmol.util.Matrix3f: Sets the specified row of this matrix3d to the three values provided.
setRow(int, float[]) - Method in class org.jmol.util.Matrix4f: Sets the specified row of this matrix4f to the four values provided.
setRowA(int, float[]) - Method in class org.jmol.util.Matrix3f: Sets the specified row of this matrix3d to the four values provided.
setRowHeaders(String[]) - Method in class etomica.data.types.DataTable.DataInfoTableFactory: Sets the row headers.
setRowLabelColumnHeader(String) - Method in class etomica.graphics.DisplayTable: Sets the header of the row-label column.
setRowLabels(String[]) - Method in class etomica.graphics.DisplayTable: Sets values for descriptive text for each row (as defined before transpose).
setRowV(int, Vector3f) - Method in class org.jmol.util.Matrix3f: Sets the specified row of this matrix3d to the Vector provided.
setRPow(double) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
setRun(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setRun(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setS(int) - Static method in class etomica.potential.P2O2Bartolomei
setSafetyFactor(double) - Method in class etomica.nbr.CriterionPositionWall: Sets the safety factor (between 0 and 1.0) that determines when the criterion thinks it needs an update.
setSafetyFactor(double) - Method in class etomica.nbr.CriterionSimple
setSafetyFactor(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular: Sets the safety factor.
setSafetyFactor(double) - Method in class etomica.nbr.list.PotentialMasterList: Sets the safety factor.
setSafetyFactor(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
setSameFileEachTime(boolean) - Method in class etomica.data.DataLogger: Write to the same file at each time INTERVAL, and close the file at the end of the simulation.
setSampleClusters(ClusterWeight[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
setSampledSwitchFrac(double) - Method in class etomica.normalmode.MeterOverlapSwitch
setSaveValues(JButton) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
setScale(double) - Method in class etomica.action.BoxInflate: Sets the scale defining the amount of inflation.
setScale(double) - Method in class etomica.graphics.DisplayBox
setScale(double) - Method in class etomica.graphics.DisplayPolytope
setScale(float) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to a scale matrix with the passed scale amount.
setSCF(boolean) - Method in class etomica.potential.P2QChemInterpolated
setSearchLimit(int) - Method in class etomica.kmc.IntegratorKMC
setSecurityOff(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets whether or not scripts should be run securely
setSeed(long) - Method in class etomica.util.MersenneTwister: Initalize the pseudo random number generator.
setSeed(long) - Method in class etomica.util.MersenneTwisterFast: Initalize the pseudo random number generator.
setSeed(int) - Method in class etomica.util.RandomMersenneTwister: Configures the RNG with the given seed.
setSeedArray(int[]) - Method in class etomica.util.RandomMersenneTwister: Configures the RNG with an array of seeds
setSeeds(int[]) - Method in class etomica.virial.simulations.SimulationVirial
setSeen(int) - Method in class etomica.graph.traversal.AbstractTraversal
setSelected(String) - Method in class etomica.graphics.DeviceButtonGroup: Selects the button with the given label.
setSelected(int) - Method in class etomica.graphics.DeviceButtonGroup: Selects ith radio button.
setSelected(int) - Method in class etomica.graphics.DeviceSelector: Sets the i-th item (counting from 0) in the list as the one currently selected.
setSelected(int) - Method in class etomica.graphics.DeviceThermoSelector: Sets the i-th item (counting from 0) in the list as the one currently selected.
setSelectedFloats(float, BitSet, float[]) - Static method in class org.jmol.util.Parser
setSelectedSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSelectedValue(int, ScriptVariable) - Method in class org.jmol.script.ScriptVariable
setShakeTolerance(double) - Method in class etomica.integrator.IntegratorVelocityVerletShake
setShape(Shape) - Method in class etomica.atom.AtomFilterInShape
setShape(Polytope) - Method in class etomica.data.meter.MeterLocalDensity
setShape(Polytope) - Method in class etomica.data.meter.MeterLocalMoleFraction: Sets the subvolume shape for the mole fraction calculation.
setShape(String) - Method in class etomica.graphics.DeviceTrioControllerButton: Sets display shape of the device.
setShapeOrigin(IVector) - Method in class etomica.data.meter.MeterLocalMoleFraction: Sets the origin of the subvolume (Polytopes typically have their center at 0).
setShearRateNumber(double) - Method in class etomica.modules.rheology.IntegratorPolymer
setShift(IVector) - Method in class etomica.interfacial.WriteConfigurationInterfacial
setShiftX(float) - Method in class etomica.graphics.DisplayCanvas
setShiftY(float) - Method in class etomica.graphics.DisplayCanvas
setShowBorder(boolean) - Method in class etomica.graphics.DeviceSlider
setShowBorder(boolean) - Method in class etomica.graphics.DeviceSpinner
setShowBoundary(boolean) - Method in class etomica.graphics.DisplayBox: Set the flag indicating if the boundary should be drawn.
setShowEValvalues(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set whether the eigenvalue # text box should be displayed.
setShowingColumnHeaders(boolean) - Method in class etomica.graphics.DisplayTable
setShowingRowLabels(boolean) - Method in class etomica.graphics.DisplayTable: Mutator method for whether table should include a column of "x" values.
setShowingUnits(boolean) - Method in class etomica.graphics.DisplayTable: Flag indicating whether a units suffix applied to the column headers (or row labels, if transposing).
setShowSlider(boolean) - Method in class etomica.graphics.DeviceSlider
setShowValues(boolean) - Method in class etomica.graphics.DeviceSlider
setShowValues(boolean) - Method in class etomica.graphics.DeviceTernarySelector: Mutator method for flag indicating whether a set of boxes is displayed with labels and fraction values as text.
setShowValues(boolean) - Method in class etomica.graphics.DeviceThermoSlider: Set whether the temperature text box should be displayed.
setShowValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set whether the temperature text box should be displayed.
setShowValues(boolean) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set whether the x- and y-Cell # text box should be displayed.
setShowValues(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set whether the wavevector # text box should be displayed.
setSideLength(int) - Method in class etomica.graphics.DeviceTernarySelector: Mutator method for the length of each side of the triangle, in pixels.
setSigma(double) - Method in class etomica.graphics.ColorSchemeOverlap
setSigma(double) - Method in class etomica.modules.adsorption.EOSSW
setSigma(double) - Method in class etomica.modules.adsorption.P1Wall
setSigma(double) - Method in class etomica.modules.colloid.P1Wall
setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall: Sets the radius.
setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall: Sets the radius.
setSigma(double) - Method in class etomica.modules.sam.P1WCAWall: Sets the radius.
setSigma(double) - Method in class etomica.modules.vle.VLESim
setSigma(double) - Method in class etomica.potential.P1HardPeriodic
setSigma(double) - Method in class etomica.potential.P22CLJQ
setSigma(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
setSigma(double) - Method in class etomica.potential.P2HardAssociationCone: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeReference: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for Lennard-Jones size parameter
setSigma(double) - Method in class etomica.potential.P2HSDipole
setSigma(double) - Method in class etomica.potential.P2LennardJones: Mutator method for Lennard-Jones size parameter.
setSigma(double) - Method in class etomica.potential.P2LennardJonesDreiding: Mutator method for Lennard-Jones size parameter.
setSigma(double) - Method in class etomica.potential.P2LJDipole
setSigma(double) - Method in class etomica.potential.P2LJQ
setSigma(double) - Method in class etomica.potential.P2LJQQ
setSigma(double) - Method in class etomica.potential.P2SoftSphere: Mutator method for soft sphere size parameter.
setSigma(double) - Method in class etomica.potential.P2WCA: Mutator method for Lennard-Jones size parameter.
setSigma(double) - Method in class etomica.rotation.P2LJDipole
setSigma(double) - Method in class etomica.units.systems.LJ
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
setSigma(double) - Method in class etomica.virial.MayerEHardSphere: Sets the HS diameter.
setSigma(double) - Method in class etomica.virial.MayerHardSphere: Sets the HS diameter.
setSigma(double) - Method in class etomica.yukawa.P2HC2Yukawa
setSigmaColloid(double) - Method in class etomica.modules.colloid.ConfigurationColloid
setSigmaHSRef(double, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
setSigmaHSRefField(JTextField, int) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
setSigmaMonomer(double) - Method in class etomica.modules.colloid.ConfigurationColloid
setSimEnvController(ControllerSimEnvironmentSelection) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
setSimulation(ISimulation, ISpace) - Method in class etomica.action.SimulationActionAdapter
setSimulation(ISimulation, ISpace, IController) - Method in class etomica.action.SimulationRestart
setSimulation(ISimulation) - Method in class etomica.box.BoxAgentManager: Sets the Simulation containing Boxs to be tracked.
setSimulation(ISimulation, ISpace, Controller) - Method in class etomica.graphics.DeviceTrioControllerButton: Sets the controller that is toggled by this device.
setSite(int[]) - Method in class etomica.lattice.RectangularLatticeNbrIterator: Identifies the site whose neighbors will be given on iteration.
setSite(String) - Method in enum etomica.virial.GUI.models.EnumSiteName
setSiteFactor(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
setSitesOnSpecies(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSize(int, int) - Method in class etomica.graphics.DeviceTable: Set the size attribute of the scrolled window the table sits on.
setSize(int, int) - Method in class etomica.graphics.DisplayPlot: Sets the drawn size of the plot
setSize(int, int) - Method in class etomica.graphics.DisplayPolytope
setSize(double[]) - Method in class etomica.lattice.crystal.Primitive: Sets the length of each primitive vector to the corresponding value in the given array.
setSize(int[]) - Method in interface etomica.lattice.FiniteLattice: Sets the array size, defined as described in the getSize method.
setSize(int) - Method in class etomica.lattice.IndexIteratorRectangular: Sets range of all indexes to the given value Indices returned vary from 0 to size-1
setSize(int[]) - Method in class etomica.lattice.IndexIteratorRectangular: Sets the individual ranges for the elements of the returned array.
setSize(int[]) - Method in interface etomica.lattice.IndexIteratorSizable: Specifies maximum index in each dimension (for dimension i, maximum index is size[i]-1).
setSize(int[]) - Method in class etomica.lattice.RectangularLattice: Sets the number lattice size (specified via the largest index in each dimension), and rebuilds the all sites using the site factory.
setSize(int, int) - Method in class etomica.modules.clustergenerator.Plot: Sets width and height of plot in pixels.
setSize(int[]) - Method in interface g3dsys.control.IndexIterator: Sets the size of each dimension; in general they should all be the same size.
setSize(int) - Method in class org.jmol.util.Quadric
setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal: Sets A to the given value and B to 2.0/sqrt(3.0)*A
setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
setSizeABC(double) - Method in class etomica.lattice.crystal.PrimitiveCubic: Sets the length of all primitive vectors to the given value.
setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
setSlab(double) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys: Set slab percentage
setSlab(double) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys: Set slab percentage
setSlab(int) - Method in class org.jmol.util.GData: clipping from the front and the back
setSlab(BitSet, BitSet, String, String, float) - Method in class org.jmol.util.MeshSurface
setSlabEnabled(boolean) - Method in class g3dsys.control.TransformManager: Enable/disable slab and depth
setSlabPercent(float) - Method in class g3dsys.control.G3DSys
setSleepPeriod(int) - Method in class etomica.action.activity.ActivityIntegrate: Sets amount of time that thread is kept in sleep state after each doStep done on integrator.
setSliderMajorValues(int) - Method in class etomica.graphics.DeviceThermoSlider: Set the number of "major" values that should be shown on the temperature slider.
setSliderMajorValues(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the number of "major" values that should be shown on the temperature slider.
setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider: Set the number of "major" values that should be shown on the n- CellNum slider.
setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the number of "major" values that should be shown on the x- and y- CellNum slider.
setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the number of "major" values that should be shown on the eigenvalue slider.
setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the number of "major" values that should be shown on the temperature slider.
setSliderMinorValues(int) - Method in class etomica.graphics.DeviceThermoSlider
setSliderPostAction(IAction) - Method in class etomica.graphics.DeviceThermoSlider: Set the post slider value changed action.
setSliderPostAction(IAction) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the post slider value changed action.
setSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceEigenvaluesSlider: Set the post slider value changed action.
setSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the post slider value changed action.
setSliderTextboxesEditable(boolean) - Method in class etomica.graphics.DevicePlotPoints
setSliderValueShape(String) - Method in class etomica.graphics.DeviceSlider
setSliderVerticalOrientation(boolean) - Method in class etomica.graphics.DeviceSlider
setSlitDim(int) - Method in class etomica.space.BoundaryRectangularSlit: Sets the non-periodic dimension to that indicated by the given value (0 is x-dimension, 1 is y-dimension, etc.).
setSmoothedY(double[]) - Method in class etomica.util.numerical.AkimaSplineSmoother
setSnapshotTime(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the document time to seek to before rasterizing.
setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSolventThermoFrac(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: Sets the fraction of well energy that is gained by an atom pair when they hop in their well.
setSources(String[]) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the list of individual SVG sources.
setSpace(ISpace) - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory: Sets the Space
setSpace(ISpace) - Method in class etomica.data.types.DataVector.DataInfoVectorFactory: Sets the Space
setSpacePosition(double) - Method in class etomica.lattice.LatticePlane: Sets the position of the plane to be the given distance from the origin in the direction of the normal.
setSpecies(ISpecies) - Method in interface etomica.api.IAtomType
setSpecies(ISpecies) - Method in class etomica.atom.AtomSourceRandomSpecies
setSpecies(ISpecies) - Method in class etomica.atom.AtomTypeLeaf
setSpecies(ISpecies) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor: Sets the ISpecies for which the chemical potential is to be measured.
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterDensity
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterLocalMoleFraction: Accessor method to set which species mole-fraction or molar-density is averaged To set to total number density, invoke with static ALL_SPECIES field as argument
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterMoleFraction
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterNMolecules
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterProfileByAtoms
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterProfileByVolume
setSpecies(ISpecies) - Method in class etomica.data.meter.MeterWidomInsertion: Sets the species, takes a prototype molecule, and gets handle to appropriate species agent in box
setSpecies(ISpecies[]) - Method in class etomica.dimer.PotentialMasterListDimer
setSpecies(ISpecies) - Method in class etomica.graphics.DeviceNSelector
setSpecies(ISpecies) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
setSpecies(ISpecies[]) - Method in class etomica.integrator.mcmove.MCMoveSemigrand: Mutator method for the set of species that can participate in an exchange move.
setSpecies(ISpecies) - Method in class etomica.interfacial.WriteConfigurationInterfacial
setSpecies(ISpecies) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection: Sets the species, takes a prototype molecule, and gets handle to appropriate species agent in box
setSpecies(ISpecies) - Method in class etomica.liquidLJ.MeterWidomInsertionP: Sets the species, takes a prototype molecule, and gets handle to appropriate species agent in box
setSpecies(ISpecies, ISpecies) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setSpecies(ISpecies) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
setSpecies(ISpecies) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
setSpecies(ISpecies) - Method in class etomica.modules.adsorption.MyMCMove
setSpecies(ISpecies, ISpecies) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
setSpecies(ISpecies[]) - Method in class etomica.modules.chainequilibrium.MeterConversion
setSpecies(ISpecies) - Method in class etomica.modules.dcvgcmd.MyMCMove
setSpecies(String) - Method in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
setSpecies(ISpecies[]) - Method in class etomica.modules.rosmosis.MeterFlux
setSpecies(ISpecies, ISpecies) - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
setSpecies(ISpecies) - Method in class etomica.normalmode.DeviceCellNum3DSlider
setSpecies(ISpecies) - Method in class etomica.normalmode.DeviceCellNumXYSlider
setSpecies(ISpecies, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterAngleBend
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterRotateCH3
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterTorsionMulti
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleMulti
setSpecies1(ISpecies) - Method in class etomica.config.ConfigurationZincblende
setSpecies1AtomicFlag(boolean) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
setSpecies2(ISpecies) - Method in class etomica.config.ConfigurationZincblende
setSpecies2AtomicFlag(boolean) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
setSpeciesA(ISpecies, ISpecies) - Method in class etomica.config.GrainBoundaryConfiguration
setSpeciesA(ISpecies) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
setSpeciesAllocation(ISpecies, float) - Method in class etomica.config.ConfigurationLatticeWithPlane: Sets the initial allocation of the species on the left side of the plane.
setSpeciesAlreadyAdded(boolean, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSpeciesB(ISpecies, ISpecies) - Method in class etomica.config.GrainBoundaryConfiguration
setSpeciesColloid(ISpecies) - Method in class etomica.modules.colloid.NeighborListManagerColloid
setSpeciesCount1(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setSpeciesCount2(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setSpeciesCount3(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setSpeciesDataModel(IMolecularModel_SpeciesFactory, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
setSpeciesDM(ModelSelectedSpecies) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
setSpeciesIdentifier(String, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
setSpeciesIndex(int[]) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
setSpeciesIndex(int, int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
setSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
setSpeciesIndex(int[]) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
setSpeciesIndex(int, int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
setSpeciesInteractionIndex(int[][]) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
setSpeciesJList(JList) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setSpeciesJList(JList) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setSpeciesListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
setSpeciesListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setSpeciesMembrane(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setSpeciesMembrane(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSpeciesMoleculeCount(int, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
setSpeciesMonomer(ISpecies) - Method in class etomica.modules.colloid.NeighborListManagerColloid
setSpeciesRemovalMsgBox(JOptionPane) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setSpeciesSelectedIndex(int[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSpeciesSelectedIndex(int, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSpeciesSelectionChanged(boolean) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
setSpeciesSelectionDM(ModelSpeciesSelection) - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
setSpeciesSolute(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setSpeciesSolute1(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSpeciesSolute2(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSpeciesSolvent(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
setSpeciesSolvent(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
setSpeciesSpheres(SpeciesSpheresMono[]) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
setSpeciesTube(SpeciesTube) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
setSpecular(boolean) - Static method in class org.jmol.util.GData
setSpecularExponent(int) - Static method in class org.jmol.util.GData: log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of shades
setSpecularPercent(int) - Static method in class org.jmol.util.GData: sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything, really
setSpecularPower(int) - Static method in class org.jmol.util.GData: fractional distance to white for specular dot
setSpiffiness(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
setSpinnerPanel(JPanel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
setSpringConstant(double) - Method in class etomica.modules.materialfracture.P1Tension
setSpringConstant(double) - Method in class etomica.potential.P1Harmonic
setSpringConstant(double) - Method in class etomica.potential.P1HarmonicSite
setSpringConstant(double) - Method in class etomica.potential.P2Anharmonic: Accessor method for harmonic energy parameter
setSpringConstant(double) - Method in class etomica.potential.P2Harmonic: Accessor method for harmonic energy parameter
setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setStart(Object) - Method in class etomica.data.DataStreamAction
setStart(float, float, float) - Method in class g3dsys.images.Line
setStartAtom(int) - Method in class etomica.virial.MCMoveClusterAtomMulti
setStartConnection(int) - Method in class etomica.virial.cluster.ClusterGenerator
setStartMolecule(int) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
setState(boolean) - Method in class etomica.graphics.DeviceCheckBox: Sets the button to the given state.
setState(boolean) - Method in class etomica.graphics.DeviceToggleButton: Toggles the button to the given state.
setState(boolean) - Method in class etomica.graphics.DeviceToggleRadioButtons: Sets the button to the given state.
setStationary(boolean) - Method in class etomica.potential.P1HardMovingBoundary
setStepFactor(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
setStepFreq0(double) - Method in class etomica.virial.overlap.IntegratorOverlap
setStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
setStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveStep
setStepSize(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent: Sets the step size of the move.
setStepSizeMax(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
setStepSizeMax(double) - Method in class etomica.integrator.mcmove.MCMoveStep
setStepSizeMax(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent: Sets the maximum allowable step size.
setStepSizeMin(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
setStepSizeMin(double) - Method in class etomica.integrator.mcmove.MCMoveStep
setStepSizeMin(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent: Returns the maximum allowable steps size.
setStiffness(double, P1IntraMolecular) - Method in class etomica.virial.MCMoveChangeBondLength
setStiffness(double, double) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation: Set PI harmonic spring stiffness for given temperature and atomic mass.
setStopConnection(int) - Method in class etomica.virial.cluster.ClusterGenerator
setStopSimulation(boolean) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setSubDataInfo(IDataInfo[]) - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
setSubtractComb(boolean) - Method in class etomica.normalmode.DataSourceFE: If true, the free energy differences will not include the combinatoric contributions (they will be the free energy of defect formation).
setSulfurType(IAtomType) - Method in class etomica.modules.sam.IntegratorVelocityVerletSAM
setSum(int) - Method in class etomica.math.discrete.FixedSumIterator: Specifies the target sum that defines the iterates.
setSurfaceColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
setSurfaceDimension(int) - Method in class etomica.data.DataProcessorInterfacialTension: Sets the dimension of the surfaces.
setSurfaceYOffset(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
setSurfaceYOffset(double) - Method in class etomica.modules.sam.ConfigurationSAM
setSwitch(boolean) - Method in class etomica.models.nitrogen.PRotConstraint
setSwitchFac(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
setSwitchFac(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
setSymbols(String[]) - Method in class etomica.graphics.DeviceTernarySelector: Symbols used to label each vertex of the triangle.
setSystemSigmaHSRef(double) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setT(Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the value of the Tuple3f argument.
setT(Tuple3i) - Method in class org.jmol.util.Tuple3i: Sets the value of this tuple to the value of tuple t1.
setT1(double) - Method in class etomica.normalmode.HTTPSoftSphereApplet
setT2(double) - Method in class etomica.normalmode.HTTPSoftSphereApplet
setTA(Tuple3f, float) - Method in class org.jmol.util.Quaternion: q = (cos(theta/2), sin(theta/2) * n)
setTableColumnNames(String[]) - Method in class etomica.graphics.DevicePlotPoints: Sets the column headers to the given strings and fires an event indicating the column headers have been changed.
setTableUpdateInterval(int) - Method in class etomica.data.DataTableAverages: Sets the interval for updating the table.
setTags(DataTag[]) - Method in class etomica.data.DataInfoFactory
setTags(DataTag[]) - Method in interface etomica.data.IEtomicaDataInfoFactory: Sets the factory's tags to those in the given array.
setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupCoupled
setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupExchange
setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntragroupExchange
setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIndexList
setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntergroup: Specifies a target atom, which should appear in all iterates.
setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntragroup
setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType: Sets the target of iteration...
setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasis: Method to specify a target atom.
setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart: Method to specify a target atom.
setTarget(IAtom) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
setTarget(IAtom) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
setTarget(IAtom) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms: Sets the target of iteration...
setTarget(IAtom) - Method in interface etomica.atom.iterator.AtomsetIteratorTargetable
setTarget(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorAll: Sets the target of iteration...
setTarget(IMolecule) - Method in class etomica.atom.iterator.MoleculeIteratorMolecule: Specifies molecule returned by this iterator, as the one containing the given target atom.
setTarget(IMolecule) - Method in interface etomica.atom.iterator.MoleculesetIteratorTargetable
setTarget(IMolecule) - Method in class etomica.atom.iterator.MpiInterspecies1A: Sets the target molecule with which all pairs are formed.
setTarget(IMolecule) - Method in class etomica.atom.iterator.MpiIntraspecies1A: Sets the target molecule with which all pairs are formed.
setTarget(IMolecule) - Method in class etomica.atom.iterator.MpiMolecule: Sets target atoms and determines the pair iterator according to the value of targetAtom.
setTarget(IAtom) - Method in class etomica.atom.iterator.TripletInnerSequential
setTarget(IAtom) - Method in class etomica.data.meter.MeterPotentialEnergy
setTarget(IMolecule) - Method in class etomica.data.meter.MeterPotentialEnergy
setTarget(IAtom) - Method in class etomica.nbr.cell.Api1ACell: Sets the target molecule with which all pairs are formed.
setTarget(IMolecule) - Method in class etomica.nbr.cell.molecule.Mpi1ACell: Sets the target molecule with which all pairs are formed.
setTarget(IAtom) - Method in class etomica.nbr.site.Api1ASite: Sets the target molecule with which all pairs are formed.
setTarget(IAtom) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
setTarget(IMolecule) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
setTarget(IAtom) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
setTarget(IMolecule) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
setTarget(IAtom) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setTarget(IMolecule) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
setTarget(IAtom) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setTarget(IMolecule) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
setTarget(IAtom) - Method in class etomica.potential.PotentialMaster.AtomIterator0
setTarget(IMolecule) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
setTargetAtom(IAtom) - Method in class etomica.atom.iterator.IteratorDirective
setTargetAtom(IAtom) - Method in interface etomica.potential.IPotential0Lrc: Informs the potential of a target atom.
setTargetAtom(IAtom) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
setTargetAtom(IAtom) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
setTargetAtom(IAtom) - Method in class etomica.potential.Potential0Lrc
setTargetAvg(DataOverlap.DataSourceOverlapAvg) - Method in class etomica.overlap.DataOverlap
setTargetDataInterval(int) - Method in class etomica.normalmode.SimOverlapModule
setTargetDensity(double) - Method in class etomica.action.BoxInflate: Sets the action to change the box dimensions isotropically to achieve the given density.
setTargetH(double) - Method in class etomica.integrator.IntegratorGear4NPH
setTargetMolecule(IMolecule) - Method in class etomica.atom.iterator.IteratorDirective
setTargetMolecule(IMolecule) - Method in interface etomica.potential.IPotential0Lrc: Informs the potential of a target atom.
setTargetMolecule(IMolecule) - Method in interface etomica.potential.IPotential0MoleculeLrc: Informs the potential of a target atom.
setTargetMolecule(IMolecule) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
setTargetMolecule(IMolecule) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
setTargetMolecule(IMolecule) - Method in class etomica.potential.Potential0Lrc
setTargetP(double) - Method in class etomica.integrator.IntegratorGear4NPH
setTargetT(double) - Method in class etomica.integrator.IntegratorGear4NPH
setTemp(double) - Method in class etomica.integrator.IntegratorConNVT
setTemperature(double) - Method in class etomica.action.AtomActionRandomizeVelocity
setTemperature(double) - Method in class etomica.action.BoxQuench: Sets the quench temperature.
setTemperature(double) - Method in class etomica.action.BoxRandomizeMomenta
setTemperature(double) - Method in class etomica.action.BoxScaleMomenta
setTemperature(double) - Method in class etomica.data.meter.MeterHyperVirial
setTemperature(double) - Method in class etomica.data.meter.MeterPressure
setTemperature(double) - Method in class etomica.data.meter.MeterPressureTensor
setTemperature(double) - Method in class etomica.data.meter.MeterWidomInsertion
setTemperature(double) - Method in class etomica.densityofstate.DataProcessorPhi
setTemperature(double) - Method in class etomica.gaussianwork.MeterBoltzmannA
setTemperature(double) - Method in class etomica.gaussianwork.MeterBoltzmannB
setTemperature(double) - Method in class etomica.gaussianwork.MeterWorkABandReweighting
setTemperature(double) - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
setTemperature(double) - Method in class etomica.graphics.DeviceThermoSlider: Set the current value for the temperature slider/text box.
setTemperature(double) - Method in class etomica.integrator.IntegratorBox: Sets the temperature for this integrator
setTemperature(double) - Method in class etomica.integrator.IntegratorHard
setTemperature(double) - Method in class etomica.integrator.IntegratorMD
setTemperature(double) - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
setTemperature(double) - Method in class etomica.integrator.mcmove.MCMoveVolume: Sets the temperature so that chi can be compted in getA, avoiding potential roundoff.
setTemperature(double) - Method in class etomica.liquidLJ.MeterPU
setTemperature(double) - Method in class etomica.liquidLJ.MeterPUCut
setTemperature(double) - Method in class etomica.liquidLJ.MeterPUCutLS
setTemperature(double) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
setTemperature(double) - Method in class etomica.liquidLJ.MeterWidomInsertionP
setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedvirial.MappedUpotential
setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
setTemperature(double, P2SoftSphericalTruncated) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
setTemperature(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
setTemperature(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
setTemperature(double) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setTemperature(double) - Method in class etomica.modules.adsorption.EOSSW
setTemperature(double) - Method in class etomica.modules.adsorption.IntegratorHybrid
setTemperature(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
setTemperature(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the current value for the temperature slider/text box.
setTemperature(double) - Method in class etomica.normalmode.BoltzmannProcessor
setTemperature(double) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
setTemperature(double) - Method in class etomica.normalmode.IntegratorHarmonic
setTemperature(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
setTemperature(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
setTemperature(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
setTemperature(double) - Method in class etomica.normalmode.MCMoveHarmonic
setTemperature(double) - Method in class etomica.normalmode.MCMoveSingleMode
setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled: Sets the temperature being sampled.
setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeSolid: Sets the temperature being sampled.
setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular: Sets the temperature being sampled.
setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
setTemperature(double) - Method in class etomica.normalmode.MeterDDP
setTemperature(double) - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
setTemperature(double) - Method in class etomica.normalmode.MeterDP
setTemperature(double) - Method in class etomica.normalmode.MeterOverlapSwitch
setTemperature(double) - Method in class etomica.normalmode.MeterSolidDA
setTemperature(double) - Method in class etomica.normalmode.MeterSolidDACut
setTemperature(double) - Method in class etomica.normalmode.MeterSolidMirror
setTemperature(double) - Method in class etomica.normalmode.MeterTargetTP
setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
setTemperature(double) - Method in interface etomica.normalmode.NormalModes: Set the temperature used for calculating omega-squared.
setTemperature(double) - Method in class etomica.normalmode.NormalModes1DHR
setTemperature(double) - Method in class etomica.normalmode.NormalModes2D
setTemperature(double) - Method in class etomica.normalmode.NormalModes3D
setTemperature(double) - Method in class etomica.normalmode.NormalModesFromFile
setTemperature(double) - Method in class etomica.normalmode.NormalModesMolecular
setTemperature(double) - Method in class etomica.normalmode.NormalModesPotential
setTemperature(double) - Method in class etomica.normalmode.NormalModesSoftSpherical
setTemperature(double) - Method in class etomica.normalmode.WriteS
setTemperature(double) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
setTemperature(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
setTemperature(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
setTemperature(double) - Method in class etomica.potential.P2LJDipole: Sets the temperature used for Boltzmann-weighting of the orientational average energy used in u(double) and integral(double)
setTemperature(double) - Method in class etomica.potential.P2LJQ: Sets the temperature used for Boltzmann-weighting of the orientational average energy used in u(double) and integral(double)
setTemperature(double) - Method in class etomica.potential.P2LJQQ: Sets the temperature used for Boltzmann-weighting of the orientational average energy used in u(double) and integral(double)
setTemperature(double) - Method in class etomica.potential.P2SemiclassicalAtomic
setTemperature(double) - Method in class etomica.potential.P2SemiclassicalMolecular
setTemperature(double) - Method in class etomica.potential.PotentialCalculationPressureTensor
setTemperature(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
setTemperature(double) - Method in class etomica.veos.VanderWaals
setTemperature(double) - Method in interface etomica.virial.ClusterAbstract
setTemperature(double) - Method in class etomica.virial.ClusterChainHS
setTemperature(double) - Method in class etomica.virial.ClusterChainSoft
setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlipped
setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlippedPartial
setTemperature(double) - Method in class etomica.virial.ClusterDifference
setTemperature(double) - Method in class etomica.virial.ClusterExchange
setTemperature(double) - Method in class etomica.virial.ClusterSinglyConnected
setTemperature(double) - Method in class etomica.virial.ClusterSum
setTemperature(double) - Method in class etomica.virial.ClusterSumHS
setTemperature(double) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizable
setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
setTemperature(double) - Method in class etomica.virial.ClusterTree
setTemperature(double) - Method in class etomica.virial.ClusterWeightAbs
setTemperature(double) - Method in class etomica.virial.ClusterWeightSumWall
setTemperature(double) - Method in class etomica.virial.ClusterWeightUmbrella
setTemperature(double) - Method in class etomica.virial.ClusterWheatleyExtendSW
setTemperature(double) - Method in class etomica.virial.ClusterWheatleyHS
setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibody
setTemperature(double) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoft
setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftBD
setTemperature(double) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
setTemperature(double) - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
setTemperature(double) - Method in class etomica.virial.MCMoveChangeBondLength
setTemperature(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
setTemperature(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
setTemperatureDataSource(DataSourceUniform) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT: Sets the temperature data source to the one given.
setTemperatures(double[]) - Method in class etomica.graphics.DeviceThermoSelector
setTempZSlab(int) - Method in class org.jmol.g3d.Graphics3D
setTetherLength(double) - Method in class etomica.potential.P2Tether: Accessor method for the tether distance
setTextBackground(Color) - Method in class etomica.graphics.DeviceBox
setThermalize(IntegratorBox, double, IRandom) - Method in class etomica.modules.adsorption.P1Wall
setThermostat(IntegratorMD.ThermostatType) - Method in class etomica.integrator.IntegratorMD: Sets the type of thermostat used by the integrator.
setThermostatInterval(int) - Method in class etomica.integrator.IntegratorMD: Sets the number of integrator intervals between thermostat actions (for velocity scaling and Andersen thermostat).
setThermostatNoDrift(boolean) - Method in class etomica.integrator.IntegratorMD: Configures the thermostat to remove any net momenta imparted to the system.
setTheta(double) - Method in class etomica.association.BiasVolumeSphereOriented: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.models.water.P2HardAssociationGCPMReference: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.models.water.PNWaterGCPMThreeSite: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationCone: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeReference: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for angle (in radians) describing width of cone.
setTheta(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setTheta(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setThetaFrac(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
setThickness(double) - Method in class etomica.potential.P1HardMovingBoundary
setTHigh(double) - Method in class etomica.graphics.ColorSchemeTemperature
setThreePoints(IVector, IVector, IVector) - Method in class etomica.math.geometry.Plane: Defines the plane by specifying three points that lie in it.
setThreshold(int) - Method in class etomica.graphics.DeviceDelaySlider: You play with fire! This allows the slider to change not increase the activity integrate sleep period, but also to decrease the integrator timestep.
setTilt(double) - Method in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
setTilt(double) - Method in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
setTime(double) - Method in class etomica.integrator.IntegratorAnalytic.AtomTimeAction
setTimeDataSource(DataSourceScalar) - Method in class etomica.data.AccumulatorHistory: Sets the DataSource used for the "time" component of the history.
setTimeStep(double) - Method in class etomica.integrator.IntegratorConNVT
setTimeStep(double) - Method in class etomica.integrator.IntegratorGear4
setTimeStep(double) - Method in class etomica.integrator.IntegratorGear4NPH
setTimeStep(double) - Method in class etomica.integrator.IntegratorMD: Sets integration time step.
setTimeStep(double) - Method in class etomica.integrator.IntegratorVerlet
setTimeStep(double) - Method in class etomica.modules.rheology.IntegratorPolymer
setTitle(String) - Method in class etomica.graphics.AboutBoxWindow
setTitle(String) - Method in class etomica.graphics.DeviceTable: Set the title of the border surrounding the table.
setTitle(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
setTLow(double) - Method in class etomica.graphics.ColorSchemeTemperature
setToCenter(IVectorMutable) - Method in class etomica.math.geometry.Plane: Sets the given vector to be the point in the plane closest to the origin.
setToInitialPosition(int[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
setToInitialPosition() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
setToInitialPosition(int[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
setToInitialPosition(double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
setToInPlaneSquare(IVector, double, IVectorMutable[]) - Method in class etomica.math.geometry.Plane: Returns four points as the vertices of a square of size d centered on x0.
setToInPlaneSquare(double, IVectorMutable[]) - Method in class etomica.math.geometry.Plane: inPlaneSquare with square centered on point in plane closest to origin.
setToInPlaneVectors(IVectorMutable[]) - Method in class etomica.math.geometry.Plane: Computes and returns two unit vectors perpendicular to each other and in the plane.
setTolerance(double) - Method in class etomica.lattice.LatticePlane
setTolerance(double) - Method in class etomica.modules.interfacial.FitTanh
setTolerance(double) - Method in class etomica.surfacetension.FitTanh
setTolerance(double) - Method in class etomica.virial.ClusterWheatleyMultibody
setToNearestPoint(IVector, IVectorMutable) - Method in class etomica.math.geometry.Plane: Determines the point in the plane closest to the point x0 (first argument).
setToNormalVector(IVectorMutable) - Method in class etomica.math.geometry.Plane: Sets the given vector to be a unit normal vector to the plane and returns it.
setTopPadding(double) - Method in class etomica.interfacial.ConfigurationLammps
setTorqueSum(PotentialCalculationTorqueSum) - Method in class etomica.integrator.IntegratorRigidIterative
setTorsionpotentiala0(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala0(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setTorsionpotentiala1(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala1(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setTorsionpotentiala2(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala2(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setTorsionpotentiala3(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
setTorsionpotentiala3(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
setTotalChildren(int) - Method in class etomica.modules.sam.SpeciesAlkaneThiol
setTotalChildren(int) - Method in class etomica.species.SpeciesSpheresHetero: Sets the total number of child atoms created by this factory.
setTotalChildren(int) - Method in class etomica.virial.SpeciesAlkane
setToU(IMoleculeList, double[]) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
setToU(IMoleculeList, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setToU(IMoleculeList, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
setToU(int, double, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
setToU(double[], IVectorMutable) - Method in class etomica.models.nitrogen.TestRotationVector
setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinition: Set all the molecules in a cell to a position and orientation that corresponds to the given generalized coordinate.
setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionLeaf: Sets the position of the atom to be its lattice position plus the offset u
setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
setToU(IMoleculeList, double[]) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
setToUMoleculei(int, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
setToUMoleculei(int, double[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
setTracker(MCMoveTracker) - Method in class etomica.integrator.mcmove.MCMove
setTransformationTensor(Tensor) - Method in class etomica.models.nitrogen.AtomActionTransformed
setTransformationTensor(Tensor) - Method in class etomica.paracetamol.AtomActionTransformed
setTranslation(Vector3f) - Method in class org.jmol.util.Matrix4f: Modifies the translational components of this matrix to the values of the Vector3f argument; the other values of this matrix are not modified.
setTranslationVector(IVector) - Method in class etomica.action.AtomActionTranslateBy
setTranslucentCoverOnly(boolean) - Method in class org.jmol.g3d.Graphics3D
setTransparentCursor(Object) - Method in interface org.jmol.api.ApiPlatform
setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
setTransposed(boolean) - Method in class etomica.graphics.DisplayTable: If fillHorizontal is true, each data set fills a row; if false, data are arranged to fill columns.
setTRatio(double) - Method in class etomica.virial.MeterVirialBDBin
setTRatio(double) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
setTRatio(double) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
setTRatio(double) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
setTriangle(DeviceTernarySelector.Triangle) - Method in class etomica.graphics.DeviceTernarySelector.MyEventManager
setTrimThreshold(float) - Method in class etomica.atom.AtomArrayList
setTrimThreshold(float) - Method in class etomica.atom.MoleculeArrayList
setTrueLabel(String) - Method in class etomica.action.ActionToggle: Specifies the button's label when the toggle is set to true.
setTrueLabel(String) - Method in class etomica.graphics.DeviceToggleButton: Specifies the button's label when the toggle is set to true.
setTrueLabel(String) - Method in class etomica.graphics.DeviceToggleRadioButtons: Specifies the button's label when the toggle is set to true.
setTruncation(double) - Method in class etomica.potential.PotentialGroupSoft
setTruncationRadius(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.potential.P2MoleculeTruncated: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncated: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.potential.P2SoftTruncated: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.rotation.P2LJDipole: Mutator method for the radial cutoff distance.
setTruncationRadius(double) - Method in class etomica.space.BoundaryDeformablePeriodic
setTSelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
setTunable(boolean) - Method in class etomica.integrator.mcmove.MCMoveStepTracker: Sets a flag to indicate whether tuning of the move is to be performed Tuning adjust the step size or other property of the move with the aim of achieving a trial acceptance rate that is near to some target value.
setType(char) - Method in interface etomica.graph.model.Edge
setType(char) - Method in class etomica.graph.model.impl.EdgeImpl
setType(char) - Method in class etomica.graph.model.impl.NodeImpl
setType(char) - Method in interface etomica.graph.model.Node
setTypeMax(DataSourceUniform.LimitType) - Method in class etomica.data.DataSourceUniform: Mutator method for the type of the right limit.
setTypeMin(DataSourceUniform.LimitType) - Method in class etomica.data.DataSourceUniform: Mutator method for the type of the left limit.
setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled: Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolid: Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular: Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) - Method in class etomica.normalmode.MeterDDP: Sets a function that returns the lattice energy for a given density.
setULatFunction(Function) - Method in class etomica.normalmode.MeterDP: Sets a function that returns the lattice energy for a given density.
setULatTruncFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolid: Sets a function that returns the lattice energy for a given density using the same truncation as the potentials in the system.
setUnit(Unit) - Method in class etomica.graphics.Device
setUnit(Unit) - Method in class etomica.graphics.DeviceBox: Accessor method to set the physical units of the displayed value.
setUnit(Unit) - Method in class etomica.graphics.DeviceSlider: Override superclass setUnit method to update label when unit is changed
setUnit(Unit) - Method in class etomica.graphics.DeviceSpinner: Override superclass setUnit method to update label when unit is changed
setUnit(PrefixedUnit) - Method in class etomica.graphics.DeviceThermoSelector: Override superclass setUnit method to update label when unit is changed
setUnit(Unit) - Method in class etomica.graphics.DeviceThermoSlider: Set the unit of temperature.
setUnit(DataTag[], Unit) - Method in class etomica.graphics.DisplayPlot
setUnit(Unit) - Method in class etomica.graphics.DisplayPlot
setUnit(Unit) - Method in class etomica.graphics.DisplayScrollingGraph: Accessor method to set the physical units of the displayed value.
setUnit(DataTag[], Unit) - Method in class etomica.graphics.DisplayTable
setUnit(Unit) - Method in class etomica.graphics.DisplayTextBox: Accessor method to set the physical units of the displayed value.
setUnit(Unit) - Method in class etomica.graphics.DisplayTextBoxesCAE
setUnit(Unit) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC: Set the unit of temperature.
setUnit(Unit) - Method in interface etomica.units.Dimensioned
setup(IBox, IPotentialMaster, IMoleculeList, ISpace) - Method in class etomica.action.CalcVibrationalModes
setup() - Method in class etomica.dimer.IntegratorDimerMin
setup() - Method in class etomica.dimer.IntegratorDimerRT: Takes in a current configuration of atoms (Rc) and creates a dimer of their positions (R1 and R2).
setup() - Method in class etomica.dimer.IntegratorEnergyMap
setup(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
setup(byte, Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
setup(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.Biconnected
setup() - Method in class etomica.integrator.Integrator: Perform initialization.
setup() - Method in class etomica.integrator.IntegratorManagerMC
setup() - Method in class etomica.integrator.IntegratorMD
setup() - Method in class etomica.kmc.IntegratorKMC
setup() - Method in class etomica.kmc.IntegratorKMCCluster
setup() - Method in class etomica.modules.adsorption.IntegratorHybrid
setup() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
setup() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
setupActiveAtoms() - Method in class etomica.modules.adsorption.MyMCMove
setupActiveAtoms() - Method in class etomica.modules.dcvgcmd.MyMCMove
setupBox() - Method in class etomica.atom.AtomLeafAgentManager: Sets the Box in which this AtomAgentManager will manage Atom agents.
setupBox() - Method in class etomica.atom.MoleculeAgentManager: Sets the Box in which this AtomAgentManager will manage molecule agents.
setupData(String, Dimension) - Method in class etomica.data.DataSourceFunction: Recalculates the y values from the current x values.
setupData() - Method in class etomica.data.DataSourceRmsVelocity: Creates the data object (a DataFunction) to be returned by getData().
setupData(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength: Creates the data object (a DataFunction) to be returned by getData().
setUpdateInterval(int) - Method in class etomica.graphics.DisplayTimer: Sets the period for updating the display.
setUpdateInterval(int) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Sets the interval for which neighbor update checks are performed.
setUpdateInterval(int) - Method in class etomica.nbr.list.NeighborListManager: Sets the interval for which neighbor update checks are performed.
setUpdatingOnAnyChange(boolean) - Method in class etomica.data.DataSet: Describes protocol for firing table events that notify of column data changes.
setupIterators() - Method in class etomica.atom.iterator.ApiIntergroup
setUpperTorsLimit(double) - Method in class etomica.models.hexane.CheckCBMCHexane
setupProfileData() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
setupTargetHistogram() - Method in class etomica.virial.simulations.SimulationVirialOverlap2: Sets up a histogram for the target system that measures how often maximum separation distances are visited.
setuReactCO(double) - Method in class etomica.modules.catalysis.ReactionManagerCO
setuReactCORev(double) - Method in class etomica.modules.catalysis.ReactionManagerCO
setUseNbrLists(boolean) - Method in class etomica.nbr.PotentialMasterHybrid
setUseNumberLocalization(boolean) - Static method in class org.jmol.util.TextFormat
setUsePermutations(boolean) - Method in class etomica.virial.ClusterBonds: Sets the usePermutations flag.
setUserStylesheet(String) - Method in class etomica.graph.view.rasterizer.SVGConverter: Sets the user stylesheet.
setUseSurfaceOnly(boolean) - Method in class etomica.modules.droplet.P2Cohesion
setVA(Vector3f, float) - Method in class org.jmol.util.AxisAngle4f: Sets the value of this AxisAngle4f to the specified axis and angle.
setValidate(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter: Defines whether or not input sources should be validated in the conversion process
setValue(int) - Method in class etomica.graphics.DeviceBoxValueChangedEvent: Set the value of a DeviceBoxValueChangedEvent (should be the value of the text box)
setValue(double) - Method in class etomica.graphics.DeviceSlider
setValue(double) - Method in class etomica.graphics.DeviceSpinner
setValue(Object) - Method in class etomica.graphics.DimensionedDoubleEditor: Sets the value to the given value, which is taken to be in simulation units.
setValue(double) - Method in class etomica.graphics.DimensionedDoubleEditor: Sets the value to the given value, which is taken to be in simulation units.
setValue(double) - Method in interface etomica.modifier.Modifier: Sets the value of the property.
setValue(double) - Method in class etomica.modifier.ModifierFunctionWrapper: Applies function to given value before setting modified property.
setValue(double) - Method in class etomica.modifier.ModifierGeneral
setValue(double) - Method in class etomica.modifier.ModifierNMolecule
setValue(double) - Method in class etomica.modules.adsorption.ModifierPMu
setValue(double) - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
setValue(double) - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
setValue(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
setValue(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
setValue(double) - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
setValue(double) - Method in class etomica.modules.entropylottery.ModifierDimensions
setValue(double) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
setValue(double) - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
setValue(double) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
setValue(double) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
setValue(double) - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
setValue(double) - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
setValue(double) - Method in class etomica.normalmode.ModifierCells3D
setValue(double) - Method in class etomica.normalmode.ModifierXCells2D
setValue(double) - Method in class etomica.normalmode.ModifierYCells2D
setValue(Field, String) - Method in class etomica.util.ParameterBase
setValue(Object, Field, String) - Method in interface etomica.util.ParameterParser: Sets obj's field to appropriate value based on the given string, if this parser is appropriate for the given field, or throws an exception if it's not.
setValue(double) - Method in class etomica.virial.simulations.ModifierTPI
setValueAt(Object, int, int) - Method in class etomica.graphics.DeviceTableModelGeneric: Set the value in the given table cell.
setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
setValueForAction(double) - Method in class etomica.modifier.ModifyAction: Stores the new value to be set by the wrapped modifier.
setVaporColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
setVariable(String, Set<Graph>) - Method in interface etomica.graph.engine.Environment
setVariable(String, Set<Graph>) - Method in class etomica.graph.engine.impl.EnvironmentImpl
setVCut(double) - Method in class etomica.mappedvirial.MappedUpotential
setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
setVectorScale(IVector) - Method in class etomica.action.BoxInflate: Sets the scale defining the amount of inflation for each dimension.
setVertex1(IVector) - Method in class etomica.math.geometry.LineSegment
setVertex2(IVector) - Method in class etomica.math.geometry.LineSegment
setVFunc(PotentialCalculationMappedVirialV.VFunc) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
setViewSpeciesSelection(ViewSpeciesSelection) - Method in class etomica.virial.GUI.views.AppViewMixtureBuilder
setVisible(boolean) - Method in class etomica.graph.viewer.ClusterViewer
setVisible(boolean) - Method in class etomica.graphics.AboutBoxWindow
setVMax(double) - Method in class etomica.graphics.DisplayScrollingGraph
setVMin(double) - Method in class etomica.graphics.DisplayScrollingGraph
setVolFluctuation(boolean) - Method in class etomica.models.nitrogen.MeterNormalizedCoord
setVolume(double) - Method in class etomica.mappedvirial.MappedUpotential: Sets volume to an arbitrary value (instead of the box volume).
setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial: Sets volume to an arbitrary value (instead of the box volume).
setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV: Sets volume to an arbitrary value (instead of the box volume).
setVolumeBias(IFunction) - Method in class etomica.integrator.mcmove.MCMoveVolume
setVZero(double) - Method in class etomica.yukawa.P2Yukawa
setW(double) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
setWallDim(int) - Method in class etomica.modules.dcvgcmd.P1WCAWall
setWallDim(int) - Method in class etomica.modules.sam.P1WCAWall
setWallDim(int) - Method in class etomica.nbr.CriterionPositionWall: Sets the orientation of the wall to be perpendicular to the given dimension
setWallPosition(double) - Method in class etomica.modules.sam.P1WCAWall
setWallPosition(double) - Method in class etomica.nbr.CriterionPositionWall: Sets the position of the wall.
setWallPosition(double) - Method in class etomica.potential.P1HardMovingBoundary
setWallVelocity(double) - Method in class etomica.potential.P1HardMovingBoundary
setWaveVec(IVectorMutable[]) - Method in class etomica.data.meter.MeterStructureFactor
setWaveVector(IVector) - Method in class etomica.normalmode.MeterHarmonicCoordinate
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.IntegratorHarmonic
setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.MCMoveHarmonic
setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.MCMoveSingleMode
setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.CalcJacobian: Sets the object that defines the normal-coordinate wave vectors.
setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.MeterNormalMode: Sets the object that defines the normal-coordinate wave vectors.
setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.WriteS
setWaveVectorNum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider: Set the current value for the wavevector # slider/text box.
setWaveVectorNum(int) - Method in class etomica.normalmode.IntegratorHarmonic
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes: Set the wave vectors used by the move.
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV: Set the wave vectors that can be changed by the move.
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV: Set the wave vectors accessible to the move.
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterF
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
setWaveVectors(IVectorMutable[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
setWaveVectors(IVectorMutable[]) - Method in class etomica.normalmode.IntegratorHarmonic
setWaveVectors(IVectorMutable[]) - Method in class etomica.normalmode.MCMoveHarmonic
setWaveVectors(IVectorMutable[]) - Method in class etomica.normalmode.MCMoveSingleMode: Set the wave vectors used by the move.
setWaveVectors(IVectorMutable[], double[]) - Method in class etomica.normalmode.MeterHarmonicEnergy
setWaveVectors(IVectorMutable[], double[]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
setWeight(Rational) - Method in class etomica.virial.cluster.ClusterDiagram
setWeight(double) - Method in class etomica.virial.MeterVirialBDBin
setWeight(double) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
setWeight(double) - Method in class etomica.virial.MeterVirialBinMultiThreaded
setWeight(double) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
setWeightCoefficients(double[]) - Method in class etomica.virial.ClusterWeightUmbrella
setWeightUpdateInterval(int) - Method in class etomica.tmmc.IntegratorTMMC: Sets the number of doStep calls between updating of weights.
setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationCone: Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for attractive-well diameter divided by sigma;
setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for attractive-well diameter divided by sigma;
setWellDiameter(double) - Method in class etomica.potential.P2HardAssociation: Accessor for well-diameter.
setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationCone: Accessor method for attractive-well depth parameter.
setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites: Accessor method for attractive-well depth parameter.
setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSites: Accessor method for attractive-well depth parameter.
setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW: Accessor method for attractive-well depth parameter.
setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeOneSite: Accessor method for attractive-well depth parameter.
setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeSW: Accessor method for attractive-well depth parameter.
setWidth(float) - Method in class etomica.graph.view.rasterizer.SVGConverter: In less than or equal to zero, the width is not constrained on the output image.
setWidthHeight(boolean) - Method in class org.jmol.util.GData
setWindow(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot: Sets up a mapping from physical units to pixel units.
setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
setWireFrame(boolean) - Method in class g3dsys.images.ImageShell
setWrappedPotential(PotentialHard) - Method in class etomica.potential.P2HardWrapper
setWrappedPotential(IPotentialAtomic) - Method in class etomica.potential.P2MoleculeMonatomic
setWriteInterval(int) - Method in class etomica.data.DataLogger: Define how many number of interval events received between writings to file.
setWriteInterval(int) - Method in class etomica.zeolite.MSDCoordWriter: Equates intervalAction method variable to variable passed in from simulation class
setWriteOnFinish(IEtomicaDataSource) - Method in class etomica.data.DataLogger
setWriteOnInterval(boolean) - Method in class etomica.data.DataLogger
setWriteScale(boolean) - Method in class etomica.graphics.DisplayCanvas
setWriteVelocity(boolean) - Method in class etomica.action.WriteConfigurationDLPOLY
setWriteVelocity(boolean) - Method in class etomica.action.WriteConfigurationP2DLPOLY
setX(int, double) - Method in interface etomica.api.IVectorMutable: Sets the i-th component of the vector to the given value d.
setX(double, double, int) - Method in class etomica.data.meter.MeterPressureByVolumeChange
setX(int, double) - Method in class etomica.space1d.Vector1D
setX(int, double) - Method in class etomica.space2d.Vector2D
setX(int, double) - Method in class etomica.space3d.Vector3D
setX(int, double) - Method in class etomica.spaceNd.VectorND
setX(float) - Method in class g3dsys.images.Ball: set the x molspace position of the figure
setX(float) - Method in class g3dsys.images.Ellipse: set the x molspace position of the figure
setX0(IVector) - Method in class etomica.potential.P1Harmonic
setXCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the x-Cell # modifier object.
setXCellNum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the current value for the xCell # slider/text box.
setXComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the "x-axis" button to its selected state.
setXDataSource(DataSourceIndependent) - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory: Sets array of independent DataInfo.
setXFlipped(boolean) - Method in class g3dsys.control.G3DSys
setXicom(double[]) - Method in class etomica.util.numerical.Function1d
setXLabel(String) - Method in class etomica.graphics.DisplayPlot
setXMax(double) - Method in class etomica.data.DataSourceUniform: Mutator method for the right limit of the range.
setXMin(double) - Method in class etomica.data.DataSourceUniform: Mutator method for the left limit of the range.
setXRange(double, double, int) - Method in class etomica.integrator.mcmove.MCMoveAtomInRegion: Defines the region atoms must be selected from.
setXRange(DoubleRange) - Method in interface etomica.util.Histogram: Sets the range of x values used in the histogram (min and max).
setXRange(DoubleRange) - Method in class etomica.util.HistogramCollapsing
setXRange(DoubleRange) - Method in class etomica.util.HistogramDiscrete
setXRange(DoubleRange) - Method in class etomica.util.HistogramExpanding
setXRange(DoubleRange) - Method in class etomica.util.HistogramNotSoSimple
setXRange(DoubleRange) - Method in class etomica.util.HistogramReweightedData
setXRange(DoubleRange) - Method in class etomica.util.HistogramSimple
setXRot(float) - Method in class etomica.graphics.DisplayCanvas
setXScale(double, double, double) - Method in class etomica.graphics.DevicePlotPoints: Sets the minimum and maximum X-axis limits on the function display sliders.
setXSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the post slider value changed action.
setXUnit(Unit) - Method in class etomica.graphics.DisplayPlot: Extend superclass method to update label with change of unit.
setXYZChange() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
setY(float) - Method in class g3dsys.images.Ball: set the y molspace position of the figure
setY(float) - Method in class g3dsys.images.Ellipse: set the y molspace position of the figure
setYCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the y-Cell # modifier object.
setYCellNum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the current value for the yCell # slider/text box.
setYComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider: Set the "y-axis" button to its selected state.
setYesButton(JButton) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
setYFlipped(boolean) - Method in class g3dsys.control.G3DSys
setYRot(float) - Method in class etomica.graphics.DisplayCanvas
setYScale(double, double, double) - Method in class etomica.graphics.DevicePlotPoints: Sets the minimum and maximum Y-axis limits on the function display sliders.
setYScale(double) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
setYSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNumXYSlider
setZ(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
setZ(float) - Method in class g3dsys.images.Ball: set the z molspace position of the figure
setZ(float) - Method in class g3dsys.images.Ellipse: set the z molspace position of the figure
setZ1(double) - Method in class etomica.potential.P2ModifiedMorse
setZ2(double) - Method in class etomica.potential.P2ModifiedMorse
setZ3() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setZ4211() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setZ4220() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
setZero() - Method in class org.jmol.util.Matrix3f: Sets this matrix to all zeros.
setZero() - Method in class org.jmol.util.Matrix4f: Sets this matrix to all zeros.
setZFraction(double, double) - Method in class etomica.modules.adsorption.MyMCMove: Sets the zFraction, the fraction of the box volume into which atoms are inserted or deleted.
setZFraction(double) - Method in class etomica.modules.dcvgcmd.MyMCMove: Sets the zFraction, the fraction of the box volume into which atoms are inserted or deleted.
setZoom(float) - Method in class etomica.graphics.DisplayCanvas
setZShade(boolean, int, int, int) - Method in class org.jmol.g3d.Graphics3D
setZShade(boolean, int, int, int) - Method in class org.jmol.util.GData
sgn(double) - Static method in class etomica.math.SpecialFunctions: The sign function, returning -1 if x < 0, zero if x == 0, and +1 if x > 0.
shadeIndexLast - Static variable in class org.jmol.util.Shader
shadeIndexMax - Static variable in class org.jmol.util.Shader
shadeIndexNoisyLimit - Static variable in class org.jmol.util.Shader
shadeIndexNormal - Static variable in class org.jmol.util.Shader
Shader - Class in org.jmol.util: All static functions.
Shader() - Constructor for class org.jmol.util.Shader
shakeAgentManager - Variable in class etomica.integrator.IntegratorVelocityVerletShake
shakeTol - Variable in class etomica.integrator.IntegratorVelocityVerletShake
Shape - Interface in etomica.math.geometry: Interface for an object that defines a closed region of space.
shape - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
shape - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
shape - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
shape - Variable in class etomica.space.Boundary
shape - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
shape - Static variable in class org.jmol.script.Token
SHAPE_AXES - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_BALLS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_CARTOON - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_CONTACT - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_DOTS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_DRAW - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_ECHO - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_FRANK - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_HALOS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_HOVER - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_LABELS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MEASURES - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MIN_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_MO - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_PMESH - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_STARS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_STICKS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_STRANDS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_STRUTS - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_TRACE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JmolConstants
SHAPE_VECTORS - Static variable in class org.jmol.viewer.JmolConstants
shapeClassBases - Static variable in class org.jmol.viewer.JmolConstants
ShapeData() - Constructor for class etomica.virial.simulations.ShapeParser.ShapeData
ShapeParser - Class in etomica.virial.simulations
ShapeParser() - Constructor for class etomica.virial.simulations.ShapeParser
ShapeParser.ShapeData - Class in etomica.virial.simulations
shapes - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
shapeTokenIndex(int) - Static method in class org.jmol.viewer.JmolConstants
shareData - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
shareData - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
shearBox - Variable in class etomica.modules.rheology.RheologyGraphic
shearRate - Variable in class etomica.modules.rheology.IntegratorPolymer
sheet - Static variable in class org.jmol.script.Token
sheetsmoothing - Static variable in class org.jmol.script.Token
shift - Variable in class etomica.interfacial.ConfigurationLammps
shift - Variable in class etomica.interfacial.WriteConfigurationInterfacial
shift - Variable in class etomica.metastable.MeterDensityDistribution
shift - Variable in class etomica.models.co2.PNCO2GCPM
shift - Variable in class etomica.models.co2.PNGCPM
shift - Variable in class etomica.models.nitrogen.P2Nitrogen
shift - Variable in class etomica.models.nitrogen.P2NitrogenAB
shift - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
shift - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
shift - Variable in class etomica.models.water.P2Water3P
shift - Variable in class etomica.models.water.P2Water4P
shift - Variable in class etomica.models.water.PNWaterGCPM
shift(int) - Method in class etomica.modules.render.ParseObj.BondInfo
shift - Variable in class etomica.potential.P2CO2EMP
shift - Variable in class etomica.potential.P2SoftSphericalTruncatedShifted
shift - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
shift0 - Variable in class etomica.space.BoundaryRectangular
shift0 - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
shifted - Variable in class etomica.normalmode.SimLJVacancy.LJParams
shiftMomenta() - Method in class etomica.integrator.IntegratorMD: Subtracts velocity from all atoms such that the new net momentum of the whole system is 0.
shiftMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
show() - Method in class etomica.math.linearalgebra.Matrix
showaxes - Static variable in class org.jmol.script.Token
showBoundary - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
showboundbox - Static variable in class org.jmol.script.Token
showfrank - Static variable in class org.jmol.script.Token
showhiddenselectionhalos - Static variable in class org.jmol.script.Token
showhydrogens - Static variable in class org.jmol.script.Token
showingColumnHeaders - Variable in class etomica.graphics.DisplayTable
showingRowLabels - Variable in class etomica.graphics.DisplayTable
showingUnits - Variable in class etomica.graphics.DisplayTable
showkeystrokes - Static variable in class org.jmol.script.Token
showmeasurements - Static variable in class org.jmol.script.Token
showmultiplebonds - Static variable in class org.jmol.script.Token
shownavigationpointalways - Static variable in class org.jmol.script.Token
showNumMoleculesPlots - Variable in class etomica.modules.vle.VLE
showPlane - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
showPointInput(boolean) - Method in class etomica.graphics.DevicePlotPoints: Sets the visibility of the data point input table.
showReport(SimulationVirialOverlap2, IIntegratorListener) - Method in class etomica.virial.GUI.components.SimulationRunner
showScale(boolean) - Method in class etomica.graphics.DevicePlotPoints: Sets the visibility of the plot axis limit sliders.
showscript - Static variable in class org.jmol.script.Token
ShowStep - Class in etomica.models.hexane
ShowStep() - Constructor for class etomica.models.hexane.ShowStep
showtiming - Static variable in class org.jmol.script.Token
showunitcell - Static variable in class org.jmol.script.Token
sidechain - Static variable in class org.jmol.script.Token
sig - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
sig - Variable in class etomica.util.numerical.NonLinearCurveFitting
sig - Variable in class etomica.virial.ClusterWheatleyHS.AllSigs
sig - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
sig2 - Variable in class etomica.graphics.ColorSchemeOverlap
sig2 - Variable in class etomica.potential.P2HardSphere: Square of collisionDiameter
sigBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
sigBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
sigBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
sigBox - Variable in class etomica.modules.swmd.SwmdGraphic
sigCounter - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
sigma - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
sigma - Variable in class etomica.models.water.P2Water3P
sigma - Variable in class etomica.models.water.P2Water4P
sigma - Variable in class etomica.models.water.P2WaterTIP4PHardCore
sigma - Variable in class etomica.models.water.PNWaterGCPM
sigma - Variable in class etomica.modules.adsorption.EOSSW
sigma - Variable in class etomica.modules.adsorption.P1Wall
sigma - Variable in class etomica.modules.colloid.P1Wall
sigma - Variable in class etomica.modules.dcvgcmd.P1WCAWall
sigma - Variable in class etomica.modules.droplet.DropletAtomic
sigma - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
sigma - Variable in class etomica.modules.sam.P1WCAWall
sigma - Variable in class etomica.modules.swmd.SwmdGraphic
sigma - Variable in class etomica.modules.vle.VLESim
sigma - Variable in class etomica.normalmode.SoftSphereSolidEOS
sigma - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
sigma - Variable in class etomica.potential.P1HardPeriodic
sigma - Variable in class etomica.potential.P2ElectrostaticWithHardCore
sigma(double) - Method in class etomica.potential.P3HydrogenManzhos
sigma - Variable in class etomica.units.systems.LJ
sigma(int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate sigma(n).
sigma(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate sigma(n).
sigma() - Method in class etomica.veos.bigdecimal.Ifactor: Sum of the divisors of the number.
sigma(int) - Method in class etomica.veos.bigdecimal.Ifactor: Sum of the k-th powers of divisors of the number.
sigma - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
sigma - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
sigma - Variable in class etomica.virial.MCMoveClusterAtomHSChain
sigma - Variable in class etomica.virial.MCMoveClusterAtomHSRing
sigma - Variable in class etomica.virial.MCMoveClusterAtomHSTree
sigma - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
sigma - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
sigma - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigma0point - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigma2 - Variable in class etomica.models.water.P2Water3P
sigma2 - Variable in class etomica.models.water.P2Water4P
sigma2 - Variable in class etomica.models.water.P2WaterTIP4PHardCore
sigma2 - Variable in class etomica.modules.sam.P1WCAWall
sigma2 - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
sigma2 - Variable in class etomica.virial.MayerWell
sigmaA - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaABpoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaAll - Variable in class etomica.models.co2.PNCO2GCPM
sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaApoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaBpoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaC - Variable in class etomica.models.co2.PNCO2GCPM
sigmaC - Variable in class etomica.potential.P2CO2EMP
sigmaC2 - Variable in class etomica.potential.P2CO2EMP
sigmaCH2 - Variable in class etomica.modules.sam.Sam
sigmaCH2 - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
sigmaCH2 - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
sigmaCH2 - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
sigmaCH2 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaCH3 - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
sigmaCH3 - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
sigmaCH3 - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
sigmaCH3 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaCO - Variable in class etomica.potential.P2CO2EMP
sigmaCO2 - Variable in class etomica.potential.P2CO2EMP
sigmaColloid - Variable in class etomica.modules.colloid.ConfigurationColloid
sigmaH - Variable in class etomica.models.water.PNWaterGCPM
sigmaHC - Static variable in class etomica.potential.P2HePCKLJS
sigmaHC2 - Variable in class etomica.potential.P2HeSimplified
sigmaHS - Variable in class etomica.AlkaneEH.DHS_NVT.Param
sigmaHS - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
sigmaHS - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
sigmaHSRef - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.ReeHooverMC.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
sigmaHSRef - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
sigmaHSRef - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
sigmaHSRef - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
sigmak(BigInteger, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate sigma_k(n).
sigmaLJ - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
sigmaLJ - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
sigmaLJ - Variable in class etomica.dielectric.TIP4P_NVT
sigmaM - Variable in class etomica.models.water.PNWaterGCPM
sigmaMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
sigmaMonomer - Variable in class etomica.modules.colloid.ConfigurationColloid
sigmaN - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
sigmaO - Variable in class etomica.models.co2.PNCO2GCPM
sigmaO - Variable in class etomica.potential.P2CO2EMP
sigmaO2 - Variable in class etomica.potential.P2CO2EMP
sigmaOC - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
sigmaOH - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
sigmaSF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
sigmaSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
sigmaSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
sign(double, double) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
signature() - Method in class etomica.atom.Atom: Returns a string of digits that uniquely identifies this atom.
signature() - Method in class etomica.atom.Molecule: Returns a string of digits that uniquely identifies this atom.
signature() - Method in class etomica.units.Dimension: The signature is the exponents of each of the base dimensions forming the given dimension.
signatureMaker - Variable in class etomica.graph.iterators.filters.GlobalFilter
SignatureMaker() - Constructor for class etomica.graph.iterators.filters.GlobalFilter.SignatureMaker
signum() - Method in class etomica.veos.bigdecimal.BigSurd: The sign: 1 if the number is >0, 0 if ==0, -1 if <0
signum() - Method in class etomica.veos.bigdecimal.BigSurdVec: Sign function.
signum() - Method in class etomica.veos.bigdecimal.Rational: The sign: 1 if the number is >0, 0 if ==0, -1 if <0
Silver - Class in etomica.chem.elements: Class for the Silver element.
Silver(String) - Constructor for class etomica.chem.elements.Silver
Silver(String, double) - Constructor for class etomica.chem.elements.Silver
SILVER - Static variable in class org.jmol.util.Colix
sim - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
sim - Variable in class etomica.atom.AtomTypeAgentManager
sim - Variable in class etomica.atom.MoleculeAgentManager
sim - Variable in class etomica.atom.SpeciesAgentManager
sim - Variable in class etomica.box.BoxAgentSourceMoleculeManager
sim - Variable in class etomica.data.meter.MeterKineticEnergyRigid
sim - Variable in class etomica.data.meter.MeterTemperature
sim - Variable in class etomica.dimer.IntegratorDimerMin
sim - Variable in class etomica.dimer.IntegratorDimerRT
sim - Variable in class etomica.graphics.DisplayBox
sim - Variable in class etomica.integrator.IntegratorRigidIterative
sim - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
sim - Variable in class etomica.modules.adsorption.AdsorptionGraphic
sim - Variable in class etomica.modules.catalysis.CatalysisGraphic
sim - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
sim - Variable in class etomica.modules.catalysis.ReactionManagerCO
sim - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
sim - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
sim - Variable in class etomica.modules.colloid.ColloidGraphic
sim - Variable in class etomica.modules.crystalviewer.CrystalViewer
sim - Variable in class etomica.modules.droplet.DropletAtomicGraphic
sim - Variable in class etomica.modules.droplet.DropletGraphic
sim - Variable in class etomica.modules.ensembles.LJMCGraphic
sim - Variable in class etomica.modules.entropylottery.EntropyLotteryGraphic
sim - Variable in class etomica.modules.insertion.InsertionGraphic
sim - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
sim - Variable in class etomica.modules.ljmd.LjmdGraphic
sim - Variable in class etomica.modules.mu.MuGraphic
sim - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
sim - Variable in class etomica.modules.multiharmonic.MultiharmonicGraphic
sim - Variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
sim - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
sim - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
sim - Variable in class etomica.modules.osmosis.Osmosis
sim - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
sim - Variable in class etomica.modules.render.RenderMDGraphic
sim - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
sim - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
sim - Variable in class etomica.modules.rosmosis.MeterFlux
sim - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
sim - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
sim - Variable in class etomica.modules.sam.ConfigurationSAM
sim - Variable in class etomica.modules.sam.CriterionTether3
sim - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
sim - Variable in class etomica.modules.swmd.SwmdGraphic
sim - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
sim - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
sim - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
sim - Variable in class etomica.nbr.cell.NeighborCellManager
sim - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
sim - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
sim - Variable in class etomica.normalmode.HTTPSoftSphereApplet
sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
sim - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
sim - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
sim - Variable in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
SIM - Static variable in class etomica.units.systems.UnitSystem
Sim() - Constructor for class etomica.units.systems.UnitSystem.Sim
SIM_UNIT - Static variable in class etomica.units.Angle
SIM_UNIT - Static variable in class etomica.units.Area
SIM_UNIT - Static variable in class etomica.units.Charge: Simulation unit of charge.
SIM_UNIT - Static variable in class etomica.units.Current: Simulation unit of electrical current.
SIM_UNIT - Static variable in class etomica.units.Dipole
SIM_UNIT - Static variable in class etomica.units.ElectricPotential: Simulation unit of charge.
SIM_UNIT - Static variable in class etomica.units.Energy: The simulation unit of energy is D-A^2/ps^2.
SIM_UNIT - Static variable in class etomica.units.Force
SIM_UNIT - Static variable in class etomica.units.Fraction: The simulation unit is the Decimal.
SIM_UNIT - Static variable in class etomica.units.Length: Simulation unit for length is the angstrom.
SIM_UNIT - Static variable in class etomica.units.LuminousIntensity: The Candela unit.
SIM_UNIT - Static variable in class etomica.units.Mass: The simulation unit is the Dalton.
SIM_UNIT - Static variable in class etomica.units.Pressure: Simulation unit of pressure is (D-A/ps^2)/A^2 = D/(A-ps^2).
SIM_UNIT - Static variable in class etomica.units.Pressure2D
SIM_UNIT - Static variable in class etomica.units.Quantity: Simulation unit is Count.
SIM_UNIT - Static variable in class etomica.units.Temperature: The simulation unit for temperature, which as kT has dimensions of energy and is D-A^2/ps^2.
SIM_UNIT - Static variable in class etomica.units.Time: Simulation unit for time is the picosecond.
SIM_UNIT - Static variable in class etomica.units.Viscosity: The simulation unit is Dalton/(A-ps).
SIM_UNIT - Static variable in class etomica.units.Volume: Simulation unit of volume is cubic Angstroms.
SimBennet - Class in etomica.normalmode: Simulation to sample Bennet's Overlap Region
SimBennet(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimBennet
SimBennet.SimBennetParam - Class in etomica.normalmode
SimBennetParam() - Constructor for class etomica.normalmode.SimBennet.SimBennetParam
SimBennetParam() - Constructor for class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
SimBennetParam() - Constructor for class etomica.normalmode.SimTargetUmbrella.SimBennetParam
SimBennetParam() - Constructor for class etomica.normalmode.SimUmbrella.SimBennetParam
SimBennetParam() - Constructor for class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
SimCalcJ - Class in etomica.normalmode: Simulation class of hard spheres in 1D or 3D that calculates the dq/dx Jacobian.
SimCalcJ(Space, int) - Constructor for class etomica.normalmode.SimCalcJ
SimCalcS - Class in etomica.normalmode: MD simulation of hard spheres in 1D or 3D with tabulation of the collective-coordinate S-matrix.
SimCalcS(Space, int, double) - Constructor for class etomica.normalmode.SimCalcS
SIMCALCS - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
SIMCALCS - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
SimCalcSLJ - Class in etomica.normalmode: MD simulation of hard spheres in 1D or 3D with tabulation of the collective-coordinate S-matrix.
SimCalcSLJ(Space, int, double, double) - Constructor for class etomica.normalmode.SimCalcSLJ
SimCalcSMorse - Class in etomica.normalmode: MC simulation of Morse model in 3D with tabulation of the collective-coordinate S-matrix.
SimCalcSMorse(Space, int, double, double) - Constructor for class etomica.normalmode.SimCalcSMorse
SimCalcSSoftSphere2D - Class in etomica.normalmode: MC simulation of FCC soft-sphere model in 2D with tabulation of the collective-coordinate S-matrix.
SimCalcSSoftSphere2D(Space, int, int[], double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphere2D
SimCalcSSoftSphereFCC - Class in etomica.normalmode: MC simulation of FCC soft-sphere model in 3D with tabulation of the collective-coordinate S-matrix.
SimCalcSSoftSphereFCC(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphereFCC
SimCalcSSoftSphereFCCSuperBox - Class in etomica.normalmode: MC simulation of FCC soft-sphere model in 3D with tabulation of the collective-coordinate S-matrix.
SimCalcSSoftSphereFCCSuperBox(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
simCDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simCDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
simCDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simCDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
SimDegFreeBinning - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Output: histogram files of probability that a mode is zero Calculate free energy of solid Treats modes as degrees of freedom
SimDegFreeBinning(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimDegFreeBinning
SimDegFreeBinning.SimParam - Class in etomica.models.oneDHardRods
SimDegreeFreedom - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Output: histogram files of probability that a mode is zero Calculate free energy of solid Treats modes as degrees of freedom
SimDegreeFreedom(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom
SimDegreeFreedom.SimParam - Class in etomica.models.oneDHardRods
SimDegreeFreedom3D - Class in etomica.models.oneDHardRods: MC simulation 3D hard spheres No graphic display Output: histogram files of probability that a mode is zero Calculate free energy of solid Treats modes as degrees of freedom
SimDegreeFreedom3D(Space, int, double, int, int, String) - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom3D
SimDegreeFreedom3D.SimParam - Class in etomica.models.oneDHardRods
SimDifferentImage - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Calculate free energy of solid Treats modes as degrees of freedom; keeps one rod at each end that does not move by central image.
SimDifferentImage(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage
SimDifferentImage.SimParam - Class in etomica.models.oneDHardRods
SimDifferentImage1D - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Calculate free energy of solid Treats modes as degrees of freedom; keeps one rod at each end that does not move by central image.
SimDifferentImage1D(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1D
SimDifferentImage1D.SimParam - Class in etomica.models.oneDHardRods
SimDifferentImage1DHR - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Calculate free energy of solid Treats modes as degrees of freedom; keeps one rod at each end that does not move by central image.
SimDifferentImage1DHR(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1DHR
SimDifferentImage1DHR.SimParam - Class in etomica.models.oneDHardRods
SimDifferentImageSsFcc - Class in etomica.models.oneDHardRods: MC simulation 3D Lennard Jones FCC crystal No graphic display Uses wavevector approach Calculate free energy of solid using normal mode insertion method Treats coupling of modes as overlap variable; Generate input files with HarmonicCrystalSoftSphereFCC Uses overlap sampling.
SimDifferentImageSsFcc(Space, int[], int[], double, int, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFcc
SimDifferentImageSsFcc.SimParam - Class in etomica.models.oneDHardRods
SimDifferentImageSsFccBigCell - Class in etomica.models.oneDHardRods: MC simulation 3D Lennard Jones FCC crystal No graphic display uses single big cell approach Calculate free energy of solid using normal mode insertion method Treats coupling of modes as overlap variable; Generate input files with HarmonicCrystalSoftSphereFCC Uses overlap sampling.
SimDifferentImageSsFccBigCell(Space, int[], int[], double, int, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
SimDifferentImageSsFccBigCell.SimParam - Class in etomica.models.oneDHardRods
SimDifferentImageSsFccDoubleSize - Class in etomica.models.oneDHardRods: MC simulation 3D Lennard Jones FCC crystal No graphic display uses single big cell approach Calculate free energy of solid using normal mode insertion method Treats coupling of modes as overlap variable; Generate input files with HarmonicCrystalSoftSphereFCC Uses overlap sampling.
SimDifferentImageSsFccDoubleSize(Space, int[], int[], double, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
SimDifferentImageSsFccDoubleSize.SimParam - Class in etomica.models.oneDHardRods
SimDimerLJadatom - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom on a surface, modeled with LJ.
SimDimerLJadatom() - Constructor for class etomica.dimer.SimDimerLJadatom
SimDimerLJadatomCluster - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimDimerLJadatomCluster(Space) - Constructor for class etomica.dimer.SimDimerLJadatomCluster
SimDimerLJgb - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimDimerLJgb() - Constructor for class etomica.dimer.SimDimerLJgb
SimDimerMEAMadatom - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimDimerMEAMadatom() - Constructor for class etomica.dimer.SimDimerMEAMadatom
SimDimerMEAMadatomCluster - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimDimerMEAMadatomCluster(Space) - Constructor for class etomica.dimer.SimDimerMEAMadatomCluster
SimDimerMEAMGB - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimDimerMEAMGB(int[], int[]) - Constructor for class etomica.dimer.SimDimerMEAMGB
SimDimerMEAMGBCluster - Class in etomica.dimer: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimDimerMEAMGBCluster(Space) - Constructor for class etomica.dimer.SimDimerMEAMGBCluster
SimDirectBetaN2RP - Class in etomica.models.nitrogen: Direct Sampling for Rotational Perturbation
SimDirectBetaN2RP(Space, int, double, double, double[]) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RP
SimDirectBetaN2RP.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the SimOverlapBetaN2RP constructor
SimDirectBetaN2RPAngleToNoAngle - Class in etomica.models.nitrogen: Direct Sampling for Rotational Perturbation from NO rotational energy to constraint-angle rotational energy
SimDirectBetaN2RPAngleToNoAngle(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
SimDirectBetaN2RPInitPert - Class in etomica.models.nitrogen: Direct Sampling for Rotational Perturbation from NO rotational energy to constraint-angle rotational energy
SimDirectBetaN2RPInitPert(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
SimDirectDisorderedAlphaN2RPInitPert - Class in etomica.models.nitrogen: Direct Sampling for Rotational Perturbation from NO rotational energy to constraint-angle rotational energy
SimDirectDisorderedAlphaN2RPInitPert(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
simEigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simEigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
SimEinStep1 - Class in etomica.normalmode: Simulation that samples a composite energy function (soft sphere and Einstein crystal) and perturbs into overlap regions shared by systems with more or less soft sphere contributions.
SimEinStep1(Space, int, double, double, double, int, double, boolean) - Constructor for class etomica.normalmode.SimEinStep1
SimEinStep1.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimEinStep1HCP - Class in etomica.normalmode: Simulation that samples a composite energy function (soft sphere and Einstein crystal) and perturbs into overlap regions shared by systems with more or less soft sphere contributions.
SimEinStep1HCP(Space, int, double, double, double, int, double, double) - Constructor for class etomica.normalmode.SimEinStep1HCP
SimEinStep1HCP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimEinStep2 - Class in etomica.normalmode: Simulation that samples a composite energy function (soft sphere and Einstein crystal) and perturbs into overlap regions shared by systems with more or less soft sphere contributions.
SimEinStep2(Space, int, double, double, double, int, double, boolean) - Constructor for class etomica.normalmode.SimEinStep2
SimEinStep2.MeterPotentialEnergyComposite - Class in etomica.normalmode
SimEinStep2.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimEinStep2HCP - Class in etomica.normalmode: Simulation that samples a composite energy function (soft sphere and Einstein crystal) and perturbs into overlap regions shared by systems with more or less soft sphere contributions.
SimEinStep2HCP(Space, int, double, double, double, int, double, double) - Constructor for class etomica.normalmode.SimEinStep2HCP
SimEinStep2HCP.MeterPotentialEnergyComposite - Class in etomica.normalmode
SimEinStep2HCP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
simEventManager - Variable in class etomica.box.BoxAgentManager
SimExtensiveTest - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Output: histogram files of probability that a mode is zero Calculate free energy of solid Testing whether or not using modes as degrees of freedom is extensive.
SimExtensiveTest(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimExtensiveTest
SimExtensiveTest.SimParam - Class in etomica.models.oneDHardRods
SimFluidSoftSphere - Class in etomica.normalmode: MC simulation of soft-sphere fluid model
SimFluidSoftSphere(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimFluidSoftSphere
simGraphic - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
SimHarmonic - Class in etomica.normalmode: Simulation to sample harmonic potential
SimHarmonic(Space, int, double, String, double) - Constructor for class etomica.normalmode.SimHarmonic
SimHarmonicHexane - Class in etomica.models.hexane
SimHarmonicHexane(Space, double, int, int, int, String, double) - Constructor for class etomica.models.hexane.SimHarmonicHexane
SimHarmonicUmbrella - Class in etomica.normalmode: Simulation to sample harmonic system and perturbing into the umbrella sampling region
SimHarmonicUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimHarmonicUmbrella
SimHarmonicUmbrella.SimBennetParam - Class in etomica.normalmode
SimHSMDVacancy - Class in etomica.normalmode: Simple Lennard-Jones molecular dynamics simulation in 3D
SimHSMDVacancy(int, double, double, int, int, double) - Constructor for class etomica.normalmode.SimHSMDVacancy
SimHSMDVacancy.HSMDVParams - Class in etomica.normalmode
SimIdealGas - Class in etomica.freeenergy.npath: Simple Lennard-Jones molecular dynamics simulation in 3D
SimIdealGas(int, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimIdealGas
SimIdealGas.LjMC3DParams - Class in etomica.freeenergy.npath
simImagT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simImagT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
SimKMCLJadatom - Class in etomica.kmc: Simulation using Henkelman's Dimer method to find a saddle point for an adatom on a surface, modeled with LJ.
SimKMCLJadatom() - Constructor for class etomica.kmc.SimKMCLJadatom
SimKMCmaster - Class in etomica.kmc
SimKMCmaster(ISpace) - Constructor for class etomica.kmc.SimKMCmaster
SimKMCMEAMadatom - Class in etomica.kmc: Simulation using Henkelman's Dimer method to find a saddle point for an adatom of Sn on a surface, modeled with MEAM.
SimKMCMEAMadatom() - Constructor for class etomica.kmc.SimKMCMEAMadatom
SimKMCworker - Class in etomica.kmc
SimKMCworker(ISpace) - Constructor for class etomica.kmc.SimKMCworker
SimLJ - Class in etomica.freeenergy.npath: Simple Lennard-Jones molecular dynamics simulation in 3D
SimLJ(int, double, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimLJ
SimLJ.LjMC3DParams - Class in etomica.freeenergy.npath
SimLJHTTISuper - Class in etomica.normalmode
SimLJHTTISuper(Space, int, double, double, double, boolean, int[]) - Constructor for class etomica.normalmode.SimLJHTTISuper
SimLJHTTISuper.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimLJHTTISuperHCP - Class in etomica.normalmode
SimLJHTTISuperHCP(Space, int, double, double, double, double, boolean, int[]) - Constructor for class etomica.normalmode.SimLJHTTISuperHCP
SimLJHTTISuperHCP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimLJVacancy - Class in etomica.normalmode: Simple Lennard-Jones molecular dynamics simulation in 3D
SimLJVacancy(int, double, double, double, int, double, boolean, boolean) - Constructor for class etomica.normalmode.SimLJVacancy
SimLJVacancy.Applet - Class in etomica.normalmode
SimLJVacancy.LJParams - Class in etomica.normalmode
SimModesJ - Class in etomica.normalmode: Simulation class of hard spheres in 1D or 3D that calculates the dq/dx Jacobian.
SimModesJ(Space, int) - Constructor for class etomica.normalmode.SimModesJ
SimOverlap - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlap(Space, int, double, double, String, double) - Constructor for class etomica.normalmode.SimOverlap
SimOverlap.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapAlphaN2TP - Class in etomica.models.nitrogen: Temperature-perturbation simulation for alpha-phase Nitrogen
SimOverlapAlphaN2TP(Space, int[], double, double, double[], double[], int, double, long, double, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapAlphaN2TP
SimOverlapAlphaN2TP.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the HSMD3D constructor
SimOverlapBetaN2RP - Class in etomica.models.nitrogen
SimOverlapBetaN2RP(Space, int, double, double, double[], double, double, int) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RP
SimOverlapBetaN2RP.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the SimOverlapBetaN2RP constructor
SimOverlapBetaN2RPScaling - Class in etomica.models.nitrogen: rotational-perturbation simulation for beta-phase Nitrogen with angle scaling however, one can set parameter "doScaling" to FALSE if scaling not desirable
SimOverlapBetaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
SimOverlapBetaN2RPScaling.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapBetaN2TP - Class in etomica.models.nitrogen: Temperature-perturbation simulation for beta-phase Nitrogen
SimOverlapBetaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2TP
SimOverlapBetaN2TP.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapDisorderedAlphaN2RPScaling - Class in etomica.models.nitrogen: rotational-perturbation simulation for beta-phase Nitrogen with angle scaling however, one can set parameter "doScaling" to FALSE if scaling not desirable
SimOverlapDisorderedAlphaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapDisorderedAlphaN2TP - Class in etomica.models.nitrogen: Temperature-perturbation simulation for disordered alpha-phase Nitrogen
SimOverlapDisorderedAlphaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
SimOverlapDisorderedAlphaN2TP.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the SimOverlapBetaN2TP constructor
SimOverlapLJ - Class in etomica.normalmode: Simulation to run sampling with the LJ potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapLJ(Space, int, double, double, double) - Constructor for class etomica.normalmode.SimOverlapLJ
SimOverlapLJ.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapLJModule - Class in etomica.normalmode: Main method that constructs an overlap sampling module to calculate the free energy difference between a harmonic system and a lennard jones solid.
SimOverlapLJModule() - Constructor for class etomica.normalmode.SimOverlapLJModule
SimOverlapLJModule.APIPotentialReference - Class in etomica.normalmode
SimOverlapLJModule.APIPotentialTarget - Class in etomica.normalmode
SimOverlapLJModule.MeterPotentialEnergyDifference - Class in etomica.normalmode
SimOverlapLJModule.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapModule - Class in etomica.normalmode: Overlap sampling "module" to calculate free energy difference.
SimOverlapModule(IBox, IBox, IIntegrator, IIntegrator, IAPIPotential, IAPIPotential, double) - Constructor for class etomica.normalmode.SimOverlapModule
SimOverlapMultiHarmonic - Class in etomica.gaussianwork: MultiHarmonic Overlap Simulation a.
SimOverlapMultiHarmonic(int, double, double, double) - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonic
SimOverlapMultiHarmonic.SimOverlapParam - Class in etomica.gaussianwork
SimOverlapMultiHarmonicOptRefPref - Class in etomica.gaussianwork: MultiHarmonic Overlap Simulation a.
SimOverlapMultiHarmonicOptRefPref(int, double, double, double, double) - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
SimOverlapMultiHarmonicOptRefPref.SimOverlapParam - Class in etomica.gaussianwork
SimOverlapMultipleWaveVectors - Class in etomica.models.oneDHardRods
SimOverlapMultipleWaveVectors(Space, int, double, double, String, double, int[], int[]) - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam - Class in etomica.models.oneDHardRods
SimOverlapMultipleWaveVectorsParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
SimOverlapMultipleWaveVectorsParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
SimOverlapMultipleWV3DLJ - Class in etomica.models.oneDHardRods
SimOverlapMultipleWV3DLJ(Space, int, double, double, String, double, int[], int[]) - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam - Class in etomica.models.oneDHardRods
SimOverlapNitrogenModel - Class in etomica.models.nitrogen: Simulation to run sampling with the nitrogen model to find the free energy difference between the harmonic reference system and the target system The Bennett's Overlapping Sampling Simulation - used to check for the computation time
SimOverlapNitrogenModel(Space, int, double, String, double) - Constructor for class etomica.models.nitrogen.SimOverlapNitrogenModel
SimOverlapNitrogenModel.SimOverlapParam - Class in etomica.models.nitrogen: Inner class for parameters understood by the HSMD3D constructor
SimOverlapParam() - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.LJVacancyMin.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.MinimizeHCP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep1.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep2.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlap.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapLJ.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
SimOverlapSoftSphere - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphere(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphere
SimOverlapSoftSphere.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereDP - Class in etomica.normalmode: Simulation to run density perturbation for soft spheres.
SimOverlapSoftSphereDP(Space, int, boolean, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereDP
SimOverlapSoftSphereDP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereEin - Class in etomica.normalmode: Simulation that samples a composite energy function (soft sphere and Einstein crystal) and perturbs into overlap regions shared by systems with more or less soft sphere contributions.
SimOverlapSoftSphereEin(Space, int, double, boolean, double, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin
SimOverlapSoftSphereEin.MeterPotentialEnergyComposite - Class in etomica.normalmode
SimOverlapSoftSphereEin.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereEinHarm - Class in etomica.normalmode: Overlap sampling simulation whose target system has a composite energy function (soft sphere and Einstein crystal) and whose reference system is defined by (harmonically coupled) normal modes and Einstein crystal.
SimOverlapSoftSphereEinHarm(Space, int, double, boolean, double, double, double, int, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm
SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite - Class in etomica.normalmode
SimOverlapSoftSphereEinHarm.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereHCP - Class in etomica.normalmode: Simulation to run sampling with the soft-sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereHCP(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereHCP
SimOverlapSoftSphereHCP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereReweighting - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereReweighting(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereReweighting
SimOverlapSoftSphereReweighting.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereSoftness - Class in etomica.normalmode: Conduct Bennett's Overlap Sampling to quantify the free-energy difference between soft-sphere model with different softness Soft-Sphere potential: U = epsilon*(sigma/r)^n where n is the exponent, s = 1/n (where s is softness) epsilon and sigma is set to 1
SimOverlapSoftSphereSoftness(Space, int, double, double, double, int[], double, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereSoftness
SimOverlapSoftSphereSoftness.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereSuperBox - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereSuperBox(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereSuperBox
SimOverlapSoftSphereSuperBox.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereTP - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereTP(Space, int, boolean, boolean, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTP
SimOverlapSoftSphereTP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereTPHCP - Class in etomica.normalmode: The original Bennett's Overlapping Sampling Simulation - used to check for the computation time
SimOverlapSoftSphereTPHCP(Space, int, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPHCP
SimOverlapSoftSphereTPHCP.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSoftSphereTPSlantedBox - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSoftSphereTPSlantedBox(Space, int, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
SimOverlapSoftSphereTPSlantedBox.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSsNxy - Class in etomica.models.oneDHardRods: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSsNxy(Space, int, double, double, String, double, int, int[], double) - Constructor for class etomica.models.oneDHardRods.SimOverlapSsNxy
SimOverlapSSnxy - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimOverlapSSnxy(Space, int, double, double, String, double, int, int[]) - Constructor for class etomica.normalmode.SimOverlapSSnxy
SimOverlapSsNxy.SimOverlapParam - Class in etomica.models.oneDHardRods: Inner class for parameters understood by the HSMD3D constructor
SimOverlapSSnxy.SimOverlapParam - Class in etomica.normalmode: Inner class for parameters understood by the HSMD3D constructor
SimOverlapTPSSParams() - Constructor for class etomica.normalmode.HTTPSoftSphereApplet.SimOverlapTPSSParams
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.SimWidomMode.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
SimParam() - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
SimParams() - Constructor for class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
SimParams() - Constructor for class etomica.models.clathrates.MinimizationTIP4P.SimParams
SimParams() - Constructor for class etomica.tests.TestHSMD3D.SimParams
SimParams() - Constructor for class etomica.tests.TestLJMC3D.SimParams
SimParams() - Constructor for class etomica.tests.TestSWChain.SimParams
Simple() - Constructor for class etomica.graphics.ColorScheme.Simple
Simple(Color) - Constructor for class etomica.graphics.ColorScheme.Simple
SimpleElementForSimilarSpecies - Class in etomica.virial.GUI.components
simpleReplace(String, String, String) - Static method in class org.jmol.util.TextFormat: Does a clean replace of strFrom in str with strTo If strTo contains strFrom, then only a single pass is done.
SimpleUnit - Class in etomica.units: Superclass for all base unit classes.
SimpleUnit(Dimension, double, String, String, boolean) - Constructor for class etomica.units.SimpleUnit: Constructor.
simplifiedP3NonAdd - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
simplifiedP3NonAdd - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
simplify() - Method in class etomica.util.Rational: Simplify the rational.
simplify() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Simplify the representation.
simRealT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simRealT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
SimTarget - Class in etomica.normalmode: Simulation to run sampling with the hard sphere potential, but measuring the harmonic potential based on normal mode data from a previous simulation.
SimTarget(Space, int, double) - Constructor for class etomica.normalmode.SimTarget
SimTargetUmbrella - Class in etomica.normalmode: Simulation to sample target system and perturbing into the umbrella sampling region
SimTargetUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimTargetUmbrella
SimTargetUmbrella.SimBennetParam - Class in etomica.normalmode
simType - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
simType - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
simulation - Variable in class etomica.action.SimulationActionAdapter
simulation - Variable in class etomica.graphics.SimulationGraphic
simulation - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
simulation - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
simulation - Variable in class etomica.nbr.PotentialMasterNbr
Simulation - Class in etomica.simulation: The main class that organizes the elements of a molecular simulation.
Simulation(ISpace) - Constructor for class etomica.simulation.Simulation: Creates a new simulation using the given space
SimulationAction - Interface in etomica.action: Interface for classes that apply some elementary action (transformation) to a simulation.
SimulationActionAdapter - Class in etomica.action: Convenience class used to define a SimulationAction.
SimulationActionAdapter() - Constructor for class etomica.action.SimulationActionAdapter
SimulationAlphaNitrogenModel - Class in etomica.models.nitrogen: Simulation class for nitrogen molecules alpha-N2 crystal Structure
SimulationAlphaNitrogenModel(ISpace, int[], double, double) - Constructor for class etomica.models.nitrogen.SimulationAlphaNitrogenModel
SimulationAtomTypeEvent - Class in etomica.simulation
SimulationAtomTypeEvent(ISimulation, IAtomType) - Constructor for class etomica.simulation.SimulationAtomTypeEvent
simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in interface etomica.api.ISimulationListener
simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationAtomTypeIndexChanged(ISimulationAtomTypeIndexEvent) - Method in class etomica.box.BoxAgentManager
SimulationAtomTypeIndexEvent - Class in etomica.simulation
SimulationAtomTypeIndexEvent(ISimulation, IAtomType, int) - Constructor for class etomica.simulation.SimulationAtomTypeIndexEvent
simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in interface etomica.api.ISimulationListener
simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationAtomTypeMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.box.BoxAgentManager
SimulationBetaNitrogenModel - Class in etomica.models.nitrogen: Simulation class for nitrogen molecules beta-N2 crystal Structure
SimulationBetaNitrogenModel(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.SimulationBetaNitrogenModel
SimulationBetaNitrogenModelTest - Class in etomica.models.nitrogen: Simulation class for nitrogen molecules beta-N2 crystal Structure
SimulationBetaNitrogenModelTest(ISpace, int[], double, double, double) - Constructor for class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
simulationBoxAdded(ISimulationBoxEvent) - Method in interface etomica.api.ISimulationListener
simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationBoxAdded(ISimulationBoxEvent) - Method in class etomica.box.BoxAgentManager
SimulationBoxEvent - Class in etomica.simulation
SimulationBoxEvent(ISimulation, IBox) - Constructor for class etomica.simulation.SimulationBoxEvent
simulationBoxRemoved(ISimulationBoxEvent) - Method in interface etomica.api.ISimulationListener
simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationBoxRemoved(ISimulationBoxEvent) - Method in class etomica.box.BoxAgentManager
SimulationContainer - Interface in etomica.simulation: TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates
SimulationDataAction - Class in etomica.action: Action that performs a call to the reset() method of a set of accumulators, as specified via a list of AccumulatorManager instances.
SimulationDataAction(DataStreamAction) - Constructor for class etomica.action.SimulationDataAction
SimulationEvent - Class in etomica.simulation
SimulationEvent(ISimulation) - Constructor for class etomica.simulation.SimulationEvent
SimulationEventManager - Class in etomica.simulation
SimulationEventManager(ISimulation) - Constructor for class etomica.simulation.SimulationEventManager
SimulationGammaNitrogenModel - Class in etomica.models.nitrogen: Simulation class for nitrogen molecules gamma-N2 crystal Structure
SimulationGammaNitrogenModel(ISpace, int, double, double) - Constructor for class etomica.models.nitrogen.SimulationGammaNitrogenModel
SimulationGraphic - Class in etomica.graphics: General class for graphical presentation of the elements of a molecular simulation.
SimulationGraphic(ISimulation, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
SimulationGraphic(ISimulation, int, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
SimulationGraphic(ISimulation, String, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
SimulationGraphic(ISimulation, int, String, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
SimulationGraphic(ISimulation, String, int, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
SimulationGraphic(ISimulation, int, String, int, ISpace, Controller) - Constructor for class etomica.graphics.SimulationGraphic
SimulationIndexEvent - Class in etomica.simulation
SimulationIndexEvent(ISimulation, int) - Constructor for class etomica.simulation.SimulationIndexEvent
SimulationOrthorhombicParacetamol - Class in etomica.paracetamol: Simulation of 3D Paracetamol molecules in Form II (Orthorhombic)
SimulationOrthorhombicParacetamol(Space, int, double) - Constructor for class etomica.paracetamol.SimulationOrthorhombicParacetamol
SimulationPanel - Class in etomica.graphics: Main panel used to display the graphical elements of a simulation.
SimulationPanel() - Constructor for class etomica.graphics.SimulationPanel
SimulationPanel(String) - Constructor for class etomica.graphics.SimulationPanel
SimulationRestart - Class in etomica.action: Action that invokes reset method of all registered simulation elements, effectively initializing the entire simulation.
SimulationRestart(ISimulation, ISpace, IController) - Constructor for class etomica.action.SimulationRestart
SimulationRheology - Class in etomica.modules.rheology: Simulation for rheology module.
SimulationRheology(ISpace) - Constructor for class etomica.modules.rheology.SimulationRheology
SimulationRunner - Class in etomica.virial.GUI.components
SimulationRunner(ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.components.SimulationRunner
simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in interface etomica.api.ISimulationListener
simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationSpeciesAdded(ISimulationSpeciesEvent) - Method in class etomica.box.BoxAgentManager
SimulationSpeciesEvent - Class in etomica.simulation
SimulationSpeciesEvent(ISimulation, ISpecies) - Constructor for class etomica.simulation.SimulationSpeciesEvent
simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in interface etomica.api.ISimulationListener
simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationSpeciesIndexChanged(ISimulationSpeciesIndexEvent) - Method in class etomica.box.BoxAgentManager
SimulationSpeciesIndexEvent - Class in etomica.simulation
SimulationSpeciesIndexEvent(ISimulation, ISpecies, int) - Constructor for class etomica.simulation.SimulationSpeciesIndexEvent
simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in interface etomica.api.ISimulationListener
simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationSpeciesMaxIndexChanged(ISimulationIndexEvent) - Method in class etomica.box.BoxAgentManager
simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in interface etomica.api.ISimulationListener
simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.atom.AtomTypeAgentManager
simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.atom.MoleculeAgentManager
simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.atom.SpeciesAgentManager
simulationSpeciesRemoved(ISimulationSpeciesEvent) - Method in class etomica.box.BoxAgentManager
SimulationVirial - Class in etomica.virial.simulations: Generic simulation using Mayer sampling to evaluate cluster integrals
SimulationVirial(ISpace, ISpecies[], int[], double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
SimulationVirial(ISpace, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial: Constructor for simulation to determine the ratio between reference and target Clusters
SimulationVirial(ISpace, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
SimulationVirial(ISpace, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirial
SimulationVirial(ISpace, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirial
SimulationVirial(ISpace, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirial
SimulationVirialDiagram - Class in etomica.virial.simulations: Virial simulation using diagram sampling.
SimulationVirialDiagram(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialDiagram
SimulationVirialMultiOverlap - Class in etomica.virial.simulations
SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract, ClusterAbstract, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract, ClusterAbstract, boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract[], ClusterWeight[], boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
SimulationVirialOverlap - Class in etomica.virial.simulations
SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract, boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
SimulationVirialOverlap(Space, SpeciesFactory[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
SimulationVirialOverlap2 - Class in etomica.virial.simulations: Simulation implementing the overlap-sampling approach to evaluating a cluster diagram.
SimulationVirialOverlap2(ISpace, ISpecies, int, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2: This constructor will create your simulation class, but you may call set methods before using it.
SimulationVirialOverlap2(ISpace, ISpecies[], int[], double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2: This constructor will create your simulation class, but you may call set methods before using it.
SimulationVirialOverlap2(ISpace, ISpecies, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
SimulationVirialOverlap2(ISpace, ISpecies, double, ClusterAbstract, ClusterAbstract, boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
SimulationVirialOverlap2(ISpace, ISpecies, double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
SimulationVirialOverlap2(ISpace, ISpecies[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
SimulationVirialOverlap2(ISpace, ISpecies[], int[], double, ClusterAbstract[], ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
SimulationVirialOverlap2.BoxClusterFactory - Class in etomica.virial.simulations
SimulationVirialPT - Class in etomica.virial.simulations: Generic simulation using Mayer sampling to evaluate cluster integrals
SimulationVirialPT(Space, SpeciesFactory, double[], ClusterWeight.Factory, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialPT: Constructor for simulation to determine the ratio bewteen reference and target Clusters
SimulationVirialUmbrella - Class in etomica.virial.simulations: Simulation implementing the umbrella-sampling approach to evaluating a cluster diagram.
SimulationVirialUmbrella(Space, double, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialUmbrella
SimulationVirialUmbrella(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialUmbrella
SimulationWorker(int, int, int, MayerFunction, MayerFunction, int, double, double, double, long, ISpace, String, double, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean) - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
SimulationWorker(int, int, MayerFunction, MayerFunction, MayerFunction, double, double, double, double, long, ISpace, String, double, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean) - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
SimUmbrella - Class in etomica.normalmode: Simulation to sample Umbrella Sampling
SimUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimUmbrella
SimUmbrella.SimBennetParam - Class in etomica.normalmode
SimUmbrellaSoftSphere - Class in etomica.normalmode: Simulation to sample Umbrella Overlap Sampling The original Umbrella Sampling Simulation - used to check for the computation time
SimUmbrellaSoftSphere(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimUmbrellaSoftSphere
SimUmbrellaSoftSphere.SimBennetParam - Class in etomica.normalmode
simWaveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simWaveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
SimWidomMode - Class in etomica.models.oneDHardRods: MD simulation of hard spheres in 1D or 3D with tabulation of the collective-coordinate S-matrix.
SimWidomMode(Space, int, double, int) - Constructor for class etomica.models.oneDHardRods.SimWidomMode
SimWidomMode.SimParam - Class in etomica.models.oneDHardRods
simWVCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
simWVCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
sin() - Method in class etomica.math.Complex: Sine of this Complex number (doesn't change this Complex number).
sin(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Trigonometric sine.
sinDtheta - Variable in class etomica.dimer.IntegratorDimerMin
SineTransform - Class in etomica.util: 3D Fourier transforms of a function, f, simplify to 1D sine transforms of the auxiliary function F(r) = r*f(r) when f is spherically symmetric.
SineTransform() - Constructor for class etomica.util.SineTransform
sinGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
sinGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
singleAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
singleAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
singleAction - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
singleAction - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
SingleAssociationSiteFluid - Class in etomica.virial.simulations
SingleAssociationSiteFluid() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid
SingleAssociationSiteFluid.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleAssociationSiteFluid2 - Class in etomica.virial.simulations: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's single attraction-site model
SingleAssociationSiteFluid2() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2
SingleAssociationSiteFluid2.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleAssociationSiteFluid2Pt - Class in etomica.virial.simulations: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's single attraction-site model 2points and 3 points diagram calculation
SingleAssociationSiteFluid2Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2Pt
SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleAssociationSiteFluid3Pt - Class in etomica.virial.simulations: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's single attraction-site model 2points and 3 points diagram calculation
SingleAssociationSiteFluid3Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid3Pt
SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleAssociationSiteFluid4Points - Class in etomica.virial.simulations
SingleAssociationSiteFluid4Points() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Points
SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleAssociationSiteFluid4Pt - Class in etomica.virial.simulations: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's double attraction-site model 4points diagram calculation
SingleAssociationSiteFluid4Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Pt
SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleAssociationSiteFluidGraph - Class in etomica.virial.simulations: repulsive potential: Lennard-Jones potential attractive potential: short-handed square well potential Wertheim's single attraction-site model
SingleAssociationSiteFluidGraph() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluidGraph
SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam - Class in etomica.virial.simulations
SingleDipole - Class in etomica.rotation
SingleDipole() - Constructor for class etomica.rotation.SingleDipole
SingleDipole.Applet - Class in etomica.rotation
SingleDumbellRattle - Class in etomica.rotation
SingleDumbellRattle() - Constructor for class etomica.rotation.SingleDumbellRattle
SingleDumbellRattle.Applet - Class in etomica.rotation
SingleDumbellShake - Class in etomica.rotation
SingleDumbellShake() - Constructor for class etomica.rotation.SingleDumbellShake
SingleDumbellShake.Applet - Class in etomica.rotation
singlet - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
singlet - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
singletId(int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
SingleValueOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
SingleWater - Class in etomica.rotation
SingleWater() - Constructor for class etomica.rotation.SingleWater
SingleWater.Applet - Class in etomica.rotation
SingleWaterMatrix - Class in etomica.rotation
SingleWaterMatrix() - Constructor for class etomica.rotation.SingleWaterMatrix
SingleWaterMatrix.Applet - Class in etomica.rotation
SingleWaterRattle - Class in etomica.rotation
SingleWaterRattle() - Constructor for class etomica.rotation.SingleWaterRattle
SingleWaterRattle.Applet - Class in etomica.rotation
SingleWaterShake - Class in etomica.rotation
SingleWaterShake() - Constructor for class etomica.rotation.SingleWaterShake
SingleWaterShake.Applet - Class in etomica.rotation
sinh() - Method in class etomica.math.Complex: Hyperbolic sine of this Complex number (doesn't change this Complex number).
sinh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The hyperbolic sine.
sink - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
sink - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
sink0 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
sink0 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkDy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
sinkDy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
sinkDy2 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkDy3 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkEigen - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
sinkEy - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
sinkEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkrj - Variable in class etomica.potential.EwaldSummation
sinkSmoothed - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
sinkSmoothed - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkTrue - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkTrueEy - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
sinkWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
sinTheta - Variable in class etomica.potential.P3CPSNonAdditiveHe
sinTheta - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
sinusoidalB - Variable in class etomica.modules.sam.Sam
site(int[]) - Method in class etomica.config.ConfigurationLattice.MyLattice: Returns the same instance of IVector with each call.
site(int[]) - Method in interface etomica.lattice.AbstractLattice: Returns the site specified by the given index.
site(int[]) - Method in class etomica.lattice.BravaisLattice: Calculates and returns a vector that is the spatial position given by adding together the primitive vectors, each multiplied by the corresponding integer index given by the array argument.
site(int[]) - Method in class etomica.lattice.BravaisLatticeCrystal: Returns a Vector instance giving the location of the referenced site.
site(IVector) - Method in class etomica.lattice.CellLattice: Returns the cell in which the given point lies.
site(int[]) - Method in class etomica.lattice.RectangularLattice: Returns the instance of the object associated with the given index.
site(int[]) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice: Returns the same instance of IVector with each call.
site(int[]) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice: Returns the same instance of IVector with each call.
site - Static variable in class org.jmol.script.Token
siteat - Static variable in class etomica.potential.P2WaterPotentialsJankowski
sitebt - Static variable in class etomica.potential.P2WaterPotentialsJankowski
siteDisplacement - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
siteDisplacement - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
siteDoubles - Static variable in class etomica.models.water.P2WaterSzalewicz
siteFactor - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
siteFactory - Variable in class etomica.lattice.RectangularLattice
SiteFactory - Interface in etomica.lattice: Interface for a class that generates the sites populating a lattice.
siteID - Static variable in class etomica.models.co2.P2CO2Hellmann
siteID - Static variable in class etomica.potential.P2NitrogenHellmann
siteID - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
SiteIterator - Interface in etomica.lattice: Interface for objects that iterate over some or all of the sites of a lattice.
siteManager - Variable in class etomica.normalmode.CoordinateDefinition
sitePos - Variable in class etomica.models.co2.P2CO2H2OWheatley
sitePos - Variable in class etomica.models.water.P2WaterSzalewicz
sitePos3 - Variable in class etomica.models.water.P2WaterSzalewicz
sitePosA - Static variable in class etomica.potential.P2NitrogenHellmann
sitePosA - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
sitePosB - Static variable in class etomica.potential.P2NitrogenHellmann
sitePosB - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
sites() - Method in interface etomica.lattice.FiniteLattice: Returns an array containing all the sites in the lattice.
sites - Variable in class etomica.lattice.RectangularLattice
sites() - Method in class etomica.lattice.RectangularLattice
sites - Static variable in class etomica.models.water.P2WaterSzalewicz
sitesCO2L - Static variable in class etomica.models.co2.P2CO2H2OWheatley
sitesHH - Static variable in class etomica.models.co2.P2CO2H2OWheatley
sitesOH - Static variable in class etomica.models.co2.P2CO2H2OWheatley
SiteSource(ISpace) - Constructor for class etomica.normalmode.CoordinateDefinition.SiteSource
sixId(int, int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams: Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5) and given number of molecules (n).
sixId(int, int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT: Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5) and given number of molecules (n).
sixStart - Static variable in class etomica.virial.cluster.VirialDiagrams
sixStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
size() - Method in class etomica.atom.iterator.ANIntergroupCoupled
size() - Method in class etomica.atom.iterator.ANIntergroupExchange
size() - Method in class etomica.atom.iterator.ANIntragroupExchange
size() - Method in class etomica.atom.iterator.ApiIndexList
size() - Method in class etomica.atom.iterator.ApiInnerVariable: Returns the number of pairs given by this iterator.
size() - Method in class etomica.atom.iterator.ApiInterArrayList: Returns the number of iterates, which is list.size*(list.size-1)/2
size() - Method in class etomica.atom.iterator.ApiIntergroup: Returns the number of pairs given by this iterator.
size() - Method in class etomica.atom.iterator.ApiIntergroupCoupled: Returns the number of pairs given by this iterator.
size() - Method in class etomica.atom.iterator.ApiIntergroupExchange: Returns the number of pairs given by this iterator.
size() - Method in class etomica.atom.iterator.ApiIntraArrayList: Returns the number of iterates, which is list.size*(list.size-1)/2
size() - Method in class etomica.atom.iterator.ApiIntragroup: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType: Returns the number of iterates given by this iterator, if iterated after a call to reset().
size() - Method in class etomica.atom.iterator.AtomIteratorArrayList: Returns the number of iterates that would be given by this iterator if reset with the current list.
size() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Returns the number of iterates that iterator would give if reset and iterated in its current condition.
size() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Returns the number of iterates that would be given by this iterator if reset with the current list.
size() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
size() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
size() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
size() - Method in class etomica.atom.iterator.AtomIteratorNull
size() - Method in class etomica.atom.iterator.AtomIteratorSinglet: returns 1 if atom is not null, 0 if atom is null.
size() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
size() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
size() - Method in interface etomica.atom.iterator.AtomsetIterator: The number of iterates returned by this iterator in its current state.
size() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms: Returns the number of iterates given by this iterator, if iterated after a call to reset().
size() - Method in class etomica.atom.iterator.MoleculeIteratorAll: Returns the number of iterates given by this iterator, if iterated after a call to reset().
size() - Method in class etomica.atom.iterator.MoleculeIteratorArrayList: Returns the number of iterates that would be given by this iterator if reset with the current list.
size() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Returns the number of iterates that would be given by this iterator if reset with the current list.
size() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet: returns 1 if atom is not null, 0 if atom is null.
size() - Method in class etomica.atom.iterator.MpiInnerFixed: Returns the number of pairs given by this iterator.
size() - Method in class etomica.atom.iterator.MpiInnerVariable: Returns the number of pairs given by this iterator.
size() - Method in class etomica.atom.iterator.MpiInterArrayList: Returns the number of iterates, which is list.size*(list.size-1)/2
size() - Method in class etomica.atom.iterator.MpiInterspecies1A
size() - Method in class etomica.atom.iterator.MpiInterspeciesAA: Returns the number of iterates, which is list.size*(list.size-1)/2
size() - Method in class etomica.atom.iterator.MpiIntraArrayList: Returns the number of iterates, which is list.size*(list.size-1)/2
size() - Method in class etomica.atom.iterator.MpiIntraspecies1A: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.atom.iterator.MpiIntraspeciesAA: Returns the number of iterates, which is list.size*(list.size-1)/2
size() - Method in class etomica.atom.iterator.MpiMolecule: Returns the number of iterates that would be given when iterating after reset.
size() - Method in class etomica.atom.iterator.TripletInnerSequential
size() - Method in class etomica.graph.model.GraphList
size() - Method in class etomica.graph.model.impl.BitmapOfLongVector
size() - Method in class etomica.graph.operations.RelabelParameters
size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
size - Variable in class etomica.lattice.crystal.Primitive
size() - Method in class etomica.lattice.RectangularLattice.Iterator
size - Variable in class etomica.lattice.RectangularLattice
size() - Method in class etomica.lattice.RectangularLatticeNbrIterator: The number of iterates returned by this iterator in its current state.
size() - Method in interface etomica.lattice.SiteIterator: Returns the number of iterates that this iterator would give if reset.
size - Variable in class etomica.modules.crystalviewer.LatticeEditor
size - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
size - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
size() - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder
size() - Method in class etomica.nbr.cell.Api1ACell: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.nbr.cell.ApiAACell: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.nbr.cell.AtomIteratorCell: Returns the number of atoms the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell: Returns the number of atoms the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.nbr.cell.molecule.Mpi1ACell: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.nbr.cell.molecule.MpiAACell: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.nbr.site.Api1ASite: Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
size() - Method in class etomica.potential.P2HardBondedList.BondArrayList
size() - Method in class etomica.potential.PotentialMaster.AtomIterator0
size() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
size() - Method in class etomica.util.ObjectArrayList: Returns the number of elements in this list.
size() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Count of coefficients.
size() - Method in class org.jmol.util.BitSet: Returns the number of bits of space actually in use by this BitSet to represent bit values.
SIZE_INCREASE_RATIO - Static variable in class etomica.atom.AtomArrayList
SIZE_INCREASE_RATIO - Static variable in class etomica.atom.MoleculeArrayList
sizeCellX - Variable in class etomica.modules.sam.Sam
sizeCellZ - Variable in class etomica.modules.sam.Sam
sizeOf(Token) - Static method in class org.jmol.script.ScriptVariable
sizeOfArray() - Method in class etomica.atom.AtomArrayList
sizeOfArray() - Method in class etomica.atom.MoleculeArrayList
sizePanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
skew - Variable in class etomica.data.AccumulatorAverageCollapsingLog
SKEW - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
SKEW - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
slab - Static variable in class org.jmol.script.Token
slab - Variable in class org.jmol.util.GData
slabBrillouin(Point3f[]) - Method in class org.jmol.util.MeshSurface
slabbyatom - Static variable in class org.jmol.script.Token
slabbymolecule - Static variable in class org.jmol.script.Token
slabColix - Variable in class org.jmol.util.MeshSurface
slabenabled - Static variable in class org.jmol.script.Token
slabMeshType - Variable in class org.jmol.util.MeshSurface
slabOptions - Variable in class org.jmol.util.MeshSurface
slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSurface
slabPolygonsList(List<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
slabrange - Static variable in class org.jmol.script.Token
slabValue - Variable in class g3dsys.control.TransformManager
slanty - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
slanty - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
slider - Variable in class etomica.graphics.DeviceSlider: Subclass of Swing slider displayed to screen located in utility package
sliderA - Variable in class etomica.modules.rheology.RheologyGraphic
sliders(int, int, String, P2SquareWellBonded) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
sliders(int, int, String, P2SquareWellBonded) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
sliders(int, int, String, P2SquareWellRadical[]) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
smallmoleculemaxatoms - Static variable in class org.jmol.script.Token
smartaromatic - Static variable in class org.jmol.script.Token
smerList - Variable in class etomica.association.ColorSchemeSmer.ColorAgent
smerList - Variable in class etomica.association.ColorSchemeSmer
smerList - Variable in class etomica.association.ColorSchemeSmerByLength
smerList - Variable in class etomica.association.MCMoveAtomMonomer
smerList - Variable in class etomica.association.MCMoveAtomSmer
smerList - Variable in class etomica.association.MCMoveBiasUB
smerList - Variable in class etomica.association.MCMoveBiasUBMolecule
smerList - Variable in class etomica.association.MCMoveMoleculeMonomer
smerList - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
smerList - Variable in class etomica.association.MCMoveMoleculeSmer
smerList - Variable in class etomica.association.MCMoveRotateAssociated
smerList - Variable in class etomica.association.MCMoveSmer
smerList - Variable in class etomica.association.MCMoveSmerRotate
smerList - Variable in class etomica.association.MCMoveVolumeAssociated
smerList - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
smiles2dimageformat - Static variable in class org.jmol.script.Token
smilesurlformat - Static variable in class org.jmol.script.Token
sn - Variable in class etomica.dimer.EnergyMap
sn - Variable in class etomica.meam.MEAM_MC
sn - Variable in class etomica.meam.MEAMMd3D
Sn - Static variable in class etomica.meam.ParameterSetMEAM
sn - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
snA - Variable in class etomica.meam.MEAM_3DMDwithGB
snA - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
snA - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
snAdatom - Variable in class etomica.dimer.EnergyMap
snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
snapshotTime - Variable in class etomica.graph.view.rasterizer.SVGConverter: Document time to seek to.
snB - Variable in class etomica.meam.MEAM_3DMDwithGB
snFix - Variable in class etomica.dimer.EnergyMap
snFixedA - Variable in class etomica.meam.MEAM_3DMDwithGB
snFixedA - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
snFixedA - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
snFixedB - Variable in class etomica.meam.MEAM_3DMDwithGB
so2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
Sodium - Class in etomica.chem.elements: Class for the Sodium element.
Sodium(String) - Constructor for class etomica.chem.elements.Sodium
Sodium(String, double) - Constructor for class etomica.chem.elements.Sodium
SoftSphere3d - Class in etomica.simulation.prototypes: Simple hard-sphere Monte Carlo simulation in 2D.
SoftSphere3d(double, int, double) - Constructor for class etomica.simulation.prototypes.SoftSphere3d
SoftSphereSolidEOS - Class in etomica.normalmode: Soft-Sphere Solid Equation of State for n = 12, 9 and 6 Reference: Tan, Schultz and Kofke, J Chem.
SoftSphereSolidEOS() - Constructor for class etomica.normalmode.SoftSphereSolidEOS
SoftSphereSolidEOSCalculator - Class in etomica.normalmode
SoftSphereSolidEOSCalculator() - Constructor for class etomica.normalmode.SoftSphereSolidEOSCalculator
soluteChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
soluteChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
soluteChargeSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
soluteMoleFraction - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
soluteMoleFraction - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
soluteMoleFractionSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
soluteMoleFractionSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
solutionChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
solutionChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
solve(Matrix) - Method in class etomica.math.linearalgebra.Matrix
solve(BigInteger[][], BigInteger[]) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Solve a linear system of equations.
solveCoefficients() - Method in class etomica.util.numerical.PadeApproximation
solvent - Static variable in class org.jmol.script.Token
solventChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
solventChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
solventChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
solventChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
solventprobe - Static variable in class org.jmol.script.Token
solventproberadius - Static variable in class org.jmol.script.Token
solventThermoFrac - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
sort() - Method in class etomica.graph.model.GraphList
sort(int[], int) - Method in class etomica.graph.property.FactorFFT
sort() - Method in class etomica.virial.cluster.ClusterDiagram: Sorts list of connections for each node in the diagram such that mConnections[i][j] < mConnections[i][k] for k > j.
sort - Static variable in class org.jmol.g3d.Graphics3D
Sort(int) - Constructor for class org.jmol.script.ScriptVariable.Sort
sortConnections(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
sortDiagrams(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Sorts diagrams in order from most bonds to fewest bonds
sorted - Variable in class etomica.graph.model.GraphList
sortedItem(List<String>, int) - Static method in class org.jmol.util.ArrayUtil
sortKey - Variable in class etomica.util.TreeLinker
sortOrReverse(int) - Method in class org.jmol.script.ScriptVariable
source - Variable in class etomica.integrator.IntegratorEvent
sources - Variable in class etomica.graph.view.rasterizer.SVGConverter: Sources files or URLs
SOUTH - Static variable in class etomica.util.Constants.CompassDirection
space - Variable in class etomica.action.SimulationActionAdapter
space - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
space - Variable in class etomica.AlkaneEH.ConformationMethane
space - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
space - Variable in class etomica.AlkaneEH.SpeciesMethane
space - Variable in class etomica.association.BiasVolume
space - Variable in class etomica.association.BiasVolumeMolecule
space - Variable in class etomica.association.MCMoveBiasUBMolecule
space - Variable in class etomica.association.MCMoveDimer
space - Variable in class etomica.association.MCMoveDimerRotate
space - Variable in class etomica.association.MCMoveSmer
space - Variable in class etomica.association.MCMoveSmerRotate
space - Variable in class etomica.config.ConfigurationLattice
space - Variable in class etomica.config.ConformationChain
space - Variable in class etomica.config.ConformationChainLinear
space - Variable in class etomica.config.ConformationLinear
space - Variable in class etomica.config.ConformationWater
space - Variable in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
space - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
space - Variable in class etomica.data.DataProcessorInterfacialTension
space - Variable in class etomica.data.DataSourceAtomDistance
space - Variable in class etomica.data.meter.MeterDihedralAngle
space - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
space - Variable in class etomica.data.meter.MeterRDF
space - Variable in class etomica.data.meter.MeterRDFPC
space - Variable in class etomica.data.meter.MeterStructureFactor
space - Variable in class etomica.data.types.DataTensor.DataInfoTensor
space - Variable in class etomica.data.types.DataTensor.DataInfoTensorFactory
space - Variable in class etomica.data.types.DataVector.DataInfoVector
space - Variable in class etomica.data.types.DataVector.DataInfoVectorFactory
space - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
space - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
space - Variable in class etomica.graphics.DisplayBoxCanvas2D
space - Variable in class etomica.graphics.SimulationGraphic
space - Variable in class etomica.integrator.IntegratorMD
space - Variable in class etomica.integrator.IntegratorMD.VectorSource
space - Variable in class etomica.integrator.mcmove.MCMoveAtom
space - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
space - Variable in class etomica.integrator.mcmove.MCMoveDimer
space - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
space - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
space - Variable in class etomica.integrator.mcmove.MCMoveMolecule
space - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
space - Variable in class etomica.interfacial.ConfigurationLammps
space - Variable in class etomica.interfacial.MeterWallForce
space - Variable in class etomica.lattice.crystal.Primitive
space - Variable in class etomica.mappedvirial.MappedUpotential
space - Variable in class etomica.mappedvirial.MeterMappedU
space - Variable in class etomica.mappedvirial.MeterMappedVirial
space - Variable in class etomica.mappedvirial.MeterMappedVirialV
space - Variable in class etomica.mappedvirial.MeterMeanForce
space - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
space - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
space - Static variable in class etomica.math.Quaternion
space - Variable in class etomica.models.clathrates.MinimizationTIP4P
space - Variable in class etomica.models.co2.P2CO2H2OWheatley
space - Variable in class etomica.models.co2.P2CO2Hellmann
space - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
space - Variable in class etomica.models.nitrogen.ConformationNitrogen
space - Variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
space - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
space - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
space - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
space - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
space - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
space - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
space - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
space - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
space - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
space - Variable in class etomica.models.nitrogen.SpeciesN2
space - Variable in class etomica.models.nitrogen.SpeciesN2B
space - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
space - Variable in class etomica.models.nitrogen.TestRotationVector
space - Variable in class etomica.models.OPLS.ConformationAceticAcid
space - Variable in class etomica.models.OPLS.SpeciesAceticAcid
space - Variable in class etomica.models.rowley.ConformationEthanol
space - Variable in class etomica.models.rowley.ConformationMethanol
space - Variable in class etomica.models.rowley.SpeciesEthanol
space - Variable in class etomica.models.rowley.SpeciesMethanol
space - Variable in class etomica.models.traPPE.ConformationMethanol
space - Variable in class etomica.models.traPPE.SpeciesMethanol
space - Variable in class etomica.models.water.ConfigurationFileTIP4P
space - Variable in class etomica.models.water.ConformationWater3P
space - Variable in class etomica.models.water.ConformationWaterGCPM
space - Variable in class etomica.models.water.ConformationWaterTIP4P
space - Variable in class etomica.models.water.P2WaterSzalewicz
space - Variable in class etomica.models.water.SpeciesWater3P
space - Variable in class etomica.models.water.SpeciesWater3POriented
space - Variable in class etomica.models.water.SpeciesWater4P
space - Variable in class etomica.models.water.SpeciesWater4PCOM
space - Variable in class etomica.models.water.SpeciesWater4POriented
space - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
space - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
space - Variable in class etomica.modules.colloid.ConfigurationColloid
space - Variable in class etomica.modules.dcvgcmd.ConformationTube
space - Variable in class etomica.modules.materialfracture.P1Tension
space - Variable in class etomica.modules.mu.DataSourceWallPressureMu
space - Variable in class etomica.modules.sam.ConfigurationSAM
space - Variable in class etomica.modules.sam.P1Sinusoidal
space - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
space - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
space - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
space - Variable in class etomica.nbr.CriterionSimple
space - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
space - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
space - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
space - Variable in class etomica.nbr.list.PotentialMasterList
space - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
space - Variable in class etomica.normalmode.ConformationHSDimer
space - Variable in class etomica.normalmode.CoordinateDefinition
space - Variable in class etomica.normalmode.HSNPT.ActionSummer
space - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
space - Variable in class etomica.normalmode.MCMovePhaseAngle
space - Variable in class etomica.normalmode.MCMoveWV
space - Variable in class etomica.normalmode.MeterDADB
space - Variable in class etomica.normalmode.MeterSolidProps
space - Variable in class etomica.normalmode.MeterSolidPropsLJ
space - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
space - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
space - Variable in class etomica.normalmode.NormalModes2D
space - Variable in class etomica.normalmode.NormalModes3D
space - Variable in class etomica.normalmode.NormalModesMolecular
space - Variable in class etomica.normalmode.NormalModesPotential
space - Variable in class etomica.normalmode.PotentialCalculationLJSP
space - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
space - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
space - Variable in class etomica.normalmode.SpeciesHSDimer
space - Variable in class etomica.normalmode.WaveVectorFactorySimple
space - Variable in class etomica.paracetamol.ConformationParacetamol
space - Variable in class etomica.paracetamol.ConformationParacetamolMonoclinic
space - Variable in class etomica.paracetamol.ConformationParacetamolOrthorhombic
space - Variable in class etomica.paracetamol.SpeciesParacetamol
space - Variable in class etomica.parser.ParserLAMMPS.Options
space - Variable in class etomica.potential.EwaldSummation
space - Variable in class etomica.potential.EwaldSumMolecules
space - Variable in class etomica.potential.P2HardWrapper
space - Variable in class etomica.potential.P2NitrogenHellmann
space - Variable in class etomica.potential.P2O2Bartolomei
space - Variable in class etomica.potential.P2SemiclassicalAtomic
space - Variable in class etomica.potential.P2SemiclassicalMolecular
space - Variable in class etomica.potential.P2WaterPotentialsJankowski
space - Variable in class etomica.potential.P3AxilrodTeller
space - Variable in class etomica.potential.P3Induction
space - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
space - Variable in class etomica.potential.Potential
space - Variable in class etomica.potential.PotentialCalculationPressureTensor
space - Variable in class etomica.potential.PotentialMolecular
space - Variable in class etomica.simulation.Simulation
space - Variable in class etomica.space.Boundary
Space - Class in etomica.space
Space() - Constructor for class etomica.space.Space
space - Variable in class etomica.species.SpeciesOriented
space - Variable in class etomica.species.SpeciesSpheres
space - Variable in class etomica.species.SpeciesSpheresCustom
space - Variable in class etomica.species.SpeciesSpheresHetero
space - Variable in class etomica.species.SpeciesSpheresMono
space - Variable in class etomica.surfacetension.SurfaceTensionMapped
space - Variable in class etomica.virial.BoxCluster
space - Variable in class etomica.virial.ClusterCoupledFlipped
space - Variable in class etomica.virial.ClusterCoupledFlippedPartial
space - Variable in class etomica.virial.ConfigurationCluster
space - Variable in class etomica.virial.Conformation7SiteRigidSF6
space - Variable in class etomica.virial.ConformationAlkaneEH
space - Variable in class etomica.virial.ConformationAnthracene3site
space - Variable in class etomica.virial.ConformationAnthraceneTraPPE
space - Variable in class etomica.virial.ConformationCO2
space - Variable in class etomica.virial.ConformationMethane
space - Variable in class etomica.virial.ConformationNaphthaleneTraPPE
space - Variable in class etomica.virial.ConformationPh3site
space - Variable in class etomica.virial.ConformationPhenanthreneTraPPE
space - Variable in class etomica.virial.MCMoveClusterAngleBend
space - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
space - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
space - Variable in class etomica.virial.MCMoveClusterRingRegrow
space - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
space - Variable in class etomica.virial.MCMoveClusterRingScale
space - Variable in class etomica.virial.MCMoveClusterRotateCH3
space - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
space - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
space - Variable in class etomica.virial.MCMoveClusterWiggleMulti
space - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
space - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
space - Variable in class etomica.virial.Species7SiteRigidSF6
space - Variable in class etomica.virial.SpeciesAlkaneEH
space - Variable in class etomica.virial.SpeciesAnthracene3site464
space - Variable in class etomica.virial.SpeciesAnthracene3site545
space - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
space - Variable in class etomica.virial.SpeciesFactorySpheres2
space - Variable in class etomica.virial.SpeciesMethane
space - Variable in class etomica.virial.SpeciesPh3site464
space - Variable in class etomica.virial.SpeciesPh3site545
space - Variable in class etomica.virial.SpeciesTraPPEAnthracene
space - Variable in class etomica.virial.SpeciesTraPPECO2
space - Variable in class etomica.virial.SpeciesTraPPENaphthalene
space - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
Space1D - Class in etomica.space1d: Factory and methods appropriate to a 1-dimensional space.
Space2D - Class in etomica.space2d: Factory and methods appropriate to a 2-dimensional space.
Space3D - Class in etomica.space3d: Factory and methods appropriate to a 3-dimensional space.
spacefill - Static variable in class org.jmol.script.Token
SpaceLattice - Interface in etomica.lattice: Marker interface indicating that AbstractLattice.site(int[]) returns an IVector instance.
spanningVectors - Variable in class org.jmol.util.MeshSurface
spec_alternate - Static variable in class org.jmol.script.Token
spec_atom - Static variable in class org.jmol.script.Token
spec_chain - Static variable in class org.jmol.script.Token
spec_model - Static variable in class org.jmol.script.Token
spec_name_pattern - Static variable in class org.jmol.script.Token
spec_resid - Static variable in class org.jmol.script.Token
spec_seqcode - Static variable in class org.jmol.script.Token
spec_seqcode_range - Static variable in class org.jmol.script.Token
SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.Colix
SpecialFunctions - Class in etomica.math: Static-method library of various functions
specialposition - Static variable in class org.jmol.script.Token
specialRef - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
species - Variable in class etomica.AlkaneEH.DHS_NVT
species - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
species - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
species - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
species - Variable in class etomica.association.TestLJAssociationMC3D_NPT
species - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
species - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
species - Variable in class etomica.atom.AtomSourceRandomSpecies
species - Variable in class etomica.atom.iterator.MoleculeIteratorAll
species - Variable in class etomica.atom.Molecule
species - Variable in class etomica.atom.MoleculeToMoleculeListSpecies
species - Variable in class etomica.box.BoxMoleculeCountEvent
species - Variable in class etomica.config.ConfigurationZincblende
species - Variable in class etomica.data.meter.MeterProfileByAtoms
species - Variable in class etomica.data.meter.MeterProfileByVolume
species - Variable in class etomica.densityofstate.DensityOfState
species - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
species - Variable in class etomica.dielectric.DHS_NVT
species - Variable in class etomica.dielectric.DLJ_NVT_1site
species - Variable in class etomica.dielectric.TIP4P_NVT
species - Variable in class etomica.dimer.PotentialMasterListDimer
species - Variable in class etomica.freeenergy.npath.SimIdealGas
species - Variable in class etomica.freeenergy.npath.SimLJ
species - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
species - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
species - Variable in class etomica.graphics.DeviceNSelector
species - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
species - Variable in class etomica.interfacial.ConfigurationLammps
species - Variable in class etomica.interfacial.FixedWall
species - Variable in class etomica.interfacial.WriteConfigurationInterfacial
species - Variable in class etomica.liquidLJ.LjMC3D
species - Variable in class etomica.liquidLJ.LjMd3D
species - Variable in class etomica.mappedvirial.MappedU
species - Variable in class etomica.mappedvirial.MappedVirialLJ
species - Variable in class etomica.mappedvirial.MappedVirialLJVGr
species - Variable in class etomica.metastable.LJmuVT
species - Variable in class etomica.metastable.LJNPT
species - Variable in class etomica.metastable.LJNVT
species - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
species - Variable in class etomica.models.clathrates.MinimizationTIP4P
species - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
species - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
species - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
species - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
species - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
species - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
species - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
species - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
species - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
species - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
species - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
species - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
species - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
species - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
species - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
species - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
species - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
species - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
species - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
species - Variable in class etomica.models.rowley.DimerApproach
species - Variable in class etomica.models.water.TestEwaldTIP4PWater
species - Variable in class etomica.modifier.ModifierNMolecule
species - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
species - Variable in class etomica.modules.chainequilibrium.MeterConversion
species - Variable in class etomica.modules.colloid.ColloidSim
species - Variable in class etomica.modules.colloid.ConfigurationColloid
species - Variable in class etomica.modules.crystalviewer.CrystalViewer
species - Variable in class etomica.modules.crystalviewer.LatticeEditor
species - Variable in class etomica.modules.droplet.Droplet
species - Variable in class etomica.modules.droplet.DropletAtomic
species - Variable in class etomica.modules.ensembles.LJMC
species - Variable in class etomica.modules.entropylottery.EntropyLottery
species - Variable in class etomica.modules.insertion.Insertion
species - Variable in class etomica.modules.interfacial.InterfacialSW
species - Variable in class etomica.modules.ljmd.Ljmd
species - Variable in class etomica.modules.materialfracture.MaterialFracture
species - Variable in class etomica.modules.mu.MeterDensitySides
species - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
species - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
species - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
species - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
species - Variable in class etomica.modules.pistoncylinder.PistonCylinder
species - Variable in class etomica.modules.render.RenderMD: The single hard-sphere species.
species - Variable in class etomica.modules.rheology.SimulationRheology
species - Variable in class etomica.modules.rosmosis.MeterFlux
species - Variable in class etomica.modules.rosmosis.P1Tether
species - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
species - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
species - Variable in class etomica.modules.sam.MeterTilt
species - Variable in class etomica.modules.sam.Sam
species - Variable in class etomica.modules.swmd.Swmd
species - Variable in class etomica.modules.vle.VLESim
species - Variable in class etomica.normalmode.DeviceCellNum3DSlider
species - Variable in class etomica.normalmode.DeviceCellNumXYSlider
species - Variable in class etomica.normalmode.HSDimerNPT
species - Variable in class etomica.normalmode.HSNPT
species - Variable in class etomica.normalmode.HTTPSoftSphereSim
species - Variable in class etomica.normalmode.LJVacancyMin
species - Variable in class etomica.normalmode.MeterBoltzmannHTTP
species - Variable in class etomica.normalmode.MeterDDP
species - Variable in class etomica.normalmode.MeterDP
species - Variable in class etomica.normalmode.MeterPlaneSlip
species - Variable in class etomica.normalmode.MeterTargetTP
species - Variable in class etomica.normalmode.MeterTilt
species - Variable in class etomica.normalmode.MeterTiltHistogram
species - Variable in class etomica.normalmode.MeterTiltRotation
species - Variable in class etomica.normalmode.MeterTiltRotationHistogram
species - Variable in class etomica.normalmode.MeterTiltRotationStdev
species - Variable in class etomica.normalmode.ModifierCells3D
species - Variable in class etomica.normalmode.ModifierXCells2D
species - Variable in class etomica.normalmode.ModifierYCells2D
species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
species - Variable in class etomica.normalmode.NormalModesMolecular
species - Variable in class etomica.normalmode.SimBennet
species - Variable in class etomica.normalmode.SimFluidSoftSphere
species - Variable in class etomica.normalmode.SimHarmonic
species - Variable in class etomica.normalmode.SimHarmonicUmbrella
species - Variable in class etomica.normalmode.SimHSMDVacancy
species - Variable in class etomica.normalmode.SimLJHTTISuper
species - Variable in class etomica.normalmode.SimLJHTTISuperHCP
species - Variable in class etomica.normalmode.SimLJVacancy
species - Variable in class etomica.normalmode.SimTargetUmbrella
species - Variable in class etomica.normalmode.SimUmbrella
species - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
species - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
species - Variable in class etomica.paracetamol.MDParacetamolMonoclinic: The single soft-sphere species.
species - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic: The single soft-sphere species.
species - Variable in class etomica.parser.ParserLAMMPS.Stuff
species - Variable in class etomica.simulation.prototypes.ChainHSMD3D
species - Variable in class etomica.simulation.prototypes.GEMCWithRotation
species - Variable in class etomica.simulation.prototypes.HsMc2d
species - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
species - Variable in class etomica.simulation.prototypes.HSMD3D: The single hard-sphere species.
species - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
species - Variable in class etomica.simulation.prototypes.LjMd2D
species - Variable in class etomica.simulation.prototypes.LjMd3D
species - Variable in class etomica.simulation.prototypes.SoftSphere3d
species - Variable in class etomica.simulation.prototypes.SwMd2D
species - Variable in class etomica.simulation.prototypes.SWMD3D
Species - Class in etomica.species: Type for atom that is a group of other atoms, and for which its node is an instance of AtomTreeNodeGroup.
Species() - Constructor for class etomica.species.Species: Simple invokes parent constructor with same arguments.
species - Variable in class etomica.surfacetension.LJMC
species - Variable in class etomica.tests.TestHSMD3D
species - Variable in class etomica.tests.TestLJMC3D
species - Variable in class etomica.thermointegration.LjMc3D
species - Variable in class etomica.threaded.atom.LJMD3DThreaded
species - Variable in class etomica.threaded.domain.LJMD3DThreaded
species - Variable in class etomica.virial.MCMoveClusterAngleBend
species - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
species - Variable in class etomica.virial.MCMoveClusterRotateCH3
species - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
species - Variable in class etomica.virial.MCMoveClusterTorsionMulti
species - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
species - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
species - Variable in class etomica.virial.MCMoveClusterWiggleMulti
species - Variable in class etomica.virial.simulations.SimulationVirial
species - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
species - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
species - Variable in class etomica.virial.simulations.SimulationVirialPT
species - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
species - Variable in class etomica.yukawa.TestHC2YukawaMC3D
species - Variable in class etomica.yukawa.TestYukawaMC3D
species - Variable in class etomica.yukawa.TestYukawaMD3D
species - Variable in class etomica.zeolite.ZeoliteSimulation: The single hard-sphere species.
species1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
species1 - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
species1 - Variable in class etomica.simulation.prototypes.HSMD2D
SPECIES1_INDEX - Static variable in class etomica.util.Debug
species2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
species2 - Variable in class etomica.simulation.prototypes.HsMc2d
species2 - Variable in class etomica.simulation.prototypes.HSMD2D
species2 - Variable in class etomica.simulation.prototypes.SoftSphere3d
species2 - Variable in class etomica.tests.TestHSMD3D
SPECIES2_INDEX - Static variable in class etomica.util.Debug
Species7SiteRigidSF6 - Class in etomica.virial: Species SF6, 7 sites, LJ, rigid, no partial charge Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
Species7SiteRigidSF6(ISpace) - Constructor for class etomica.virial.Species7SiteRigidSF6
Species7SiteRigidSF6(ISpace, boolean) - Constructor for class etomica.virial.Species7SiteRigidSF6
speciesA - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
speciesA - Variable in class etomica.modules.adsorption.Adsorption
speciesA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
speciesA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
speciesA - Variable in class etomica.modules.mu.Mu
speciesA - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
speciesA - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
speciesA - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
SpeciesAceticAcid - Class in etomica.models.OPLS: Species for OPLS acetic acid
SpeciesAceticAcid(ISpace) - Constructor for class etomica.models.OPLS.SpeciesAceticAcid
speciesAdded(ISpecies) - Method in class etomica.simulation.SimulationEventManager
SpeciesAgentManager - Class in etomica.atom: AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents in every AtomType in a box.
SpeciesAgentManager(SpeciesAgentManager.AgentSource) - Constructor for class etomica.atom.SpeciesAgentManager
SpeciesAgentManager(SpeciesAgentManager.AgentSource, ISimulation) - Constructor for class etomica.atom.SpeciesAgentManager
speciesAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
SpeciesAgentManager.AgentIterator - Class in etomica.atom: Iterator that loops over the agents, skipping null elements
SpeciesAgentManager.AgentSource - Interface in etomica.atom: Interface for an object that wants an agent associated with each AtomType in a Simulation.
SpeciesAlkane - Class in etomica.virial
SpeciesAlkane(ISpace, int) - Constructor for class etomica.virial.SpeciesAlkane
SpeciesAlkane(ISpace, int, ElementSimple, ElementSimple) - Constructor for class etomica.virial.SpeciesAlkane
speciesAlkaneEH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
SpeciesAlkaneEH - Class in etomica.AlkaneEH: Species for TraPPE-Explicit hydrogen,Siepmann
SpeciesAlkaneEH(ISpace, int) - Constructor for class etomica.AlkaneEH.SpeciesAlkaneEH
speciesAlkaneEH - Variable in class etomica.virial.ConformationAlkaneEH
SpeciesAlkaneEH - Class in etomica.virial: Species for TraPPE-Explicit hydrogen,Siepmann
SpeciesAlkaneEH(ISpace, int) - Constructor for class etomica.virial.SpeciesAlkaneEH
SpeciesAlkaneThiol - Class in etomica.modules.sam
SpeciesAlkaneThiol(ISpace, int) - Constructor for class etomica.modules.sam.SpeciesAlkaneThiol
SpeciesAnthracene3site464 - Class in etomica.virial: Species Anthracene molecule rigid , LJ potential, no charge, this model is very similar to 3site 545 model, only the weight of the sites are different reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998 * @author shu March, 7, 2011
SpeciesAnthracene3site464(ISpace) - Constructor for class etomica.virial.SpeciesAnthracene3site464
SpeciesAnthracene3site464(ISpace, boolean) - Constructor for class etomica.virial.SpeciesAnthracene3site464
SpeciesAnthracene3site545 - Class in etomica.virial: Species Anthracene molecule rigid , LJ potential, no charge, 3 site model.each benzene ring is a site reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998 * @author shu March, 7, 2011
SpeciesAnthracene3site545(ISpace) - Constructor for class etomica.virial.SpeciesAnthracene3site545
SpeciesAnthracene3site545(ISpace, boolean) - Constructor for class etomica.virial.SpeciesAnthracene3site545
speciesB - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
speciesB - Variable in class etomica.modules.adsorption.Adsorption
speciesB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
speciesB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
speciesB - Variable in class etomica.modules.mu.Mu
speciesB - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
speciesB - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
speciesB - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
speciesBottomWall - Variable in class etomica.interfacial.LJMC
speciesBottomWall - Variable in class etomica.interfacial.LJMD
speciesC - Variable in class etomica.modules.catalysis.Catalysis
speciesC - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
speciesC - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
speciesC - Variable in class etomica.modules.catalysis.MeterDensityCO
speciesC - Variable in class etomica.modules.catalysis.MeterDensityCO2
speciesCH4 - Variable in class etomica.AlkaneEH.CH4NVT
speciesChlorine - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
speciesColloid - Variable in class etomica.modules.colloid.ColloidSim
speciesColloid - Variable in class etomica.modules.colloid.ConfigurationColloid
speciesColloid - Variable in class etomica.modules.colloid.NeighborListManagerColloid
speciesEthanol - Static variable in class etomica.models.rowley.DimerApproach
SpeciesEthanol - Class in etomica.models.rowley: Species for ethanol with satellite site (Rowley et al 2006).
SpeciesEthanol(ISpace, boolean) - Constructor for class etomica.models.rowley.SpeciesEthanol
SpeciesFactory - Interface in etomica.virial
SpeciesFactoryEthanol - Class in etomica.models.rowley: SpeciesFactory that makes ethanol.
SpeciesFactoryEthanol(boolean) - Constructor for class etomica.models.rowley.SpeciesFactoryEthanol
SpeciesFactoryMethanol - Class in etomica.models.rowley: SpeciesFactory that makes methanol.
SpeciesFactoryMethanol(boolean) - Constructor for class etomica.models.rowley.SpeciesFactoryMethanol
SpeciesFactoryMethanol - Class in etomica.models.traPPE: SpeciesFactory that makes methanol.
SpeciesFactoryMethanol() - Constructor for class etomica.models.traPPE.SpeciesFactoryMethanol
SpeciesFactoryOrientedSpheres - Class in etomica.virial: SpeciesFactory that makes SpeciesSpheresMono
SpeciesFactoryOrientedSpheres() - Constructor for class etomica.virial.SpeciesFactoryOrientedSpheres
SpeciesFactorySiepmannSpheres - Class in etomica.virial: SpeciesFactory that makes Siepmann's alkane model.
SpeciesFactorySiepmannSpheres(ISpace, int) - Constructor for class etomica.virial.SpeciesFactorySiepmannSpheres
SpeciesFactorySiepmannSpheres(ISpace, int, double, double) - Constructor for class etomica.virial.SpeciesFactorySiepmannSpheres
SpeciesFactorySpheres - Class in etomica.virial: SpeciesFactory that makes SpeciesSpheresMono
SpeciesFactorySpheres() - Constructor for class etomica.virial.SpeciesFactorySpheres
SpeciesFactorySpheres2 - Class in etomica.virial
SpeciesFactorySpheres2(ISpace, int, ElementSimple, ElementSimple) - Constructor for class etomica.virial.SpeciesFactorySpheres2
SpeciesFactorySpheres2(ISpace, int, ElementSimple, ElementSimple, double, double) - Constructor for class etomica.virial.SpeciesFactorySpheres2
SpeciesFactoryTangentSpheres - Class in etomica.virial: SpeciesFactory that makes a tangent sphere species.
SpeciesFactoryTangentSpheres(int, IConformation) - Constructor for class etomica.virial.SpeciesFactoryTangentSpheres
SpeciesFactoryWater3P - Class in etomica.virial: SpeciesFactory that makes SpeciesWater
SpeciesFactoryWater3P() - Constructor for class etomica.virial.SpeciesFactoryWater3P
SpeciesFactoryWater4P - Class in etomica.virial: SpeciesFactory that makes SpeciesWater
SpeciesFactoryWater4P(IConformation) - Constructor for class etomica.virial.SpeciesFactoryWater4P
SpeciesFactoryWaterGCPM - Class in etomica.virial: SpeciesFactory that makes SpeciesWater
SpeciesFactoryWaterGCPM() - Constructor for class etomica.virial.SpeciesFactoryWaterGCPM
speciesFluid - Variable in class etomica.interfacial.LJMC
speciesFluid - Variable in class etomica.interfacial.LJMD
speciesGhost - Variable in class etomica.modules.insertion.Insertion
SpeciesHexane - Class in etomica.models.hexane: Species used to create hexane molecules per Dr.
SpeciesHexane(ISpace) - Constructor for class etomica.models.hexane.SpeciesHexane
SpeciesHSDimer - Class in etomica.normalmode: Species hard-sphere dimer molecule
SpeciesHSDimer(ISpace) - Constructor for class etomica.normalmode.SpeciesHSDimer
SpeciesHSDimer(ISpace, boolean, double) - Constructor for class etomica.normalmode.SpeciesHSDimer
speciesIndex - Variable in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
speciesIndex - Variable in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
speciesIndexChanged(ISpecies, int) - Method in class etomica.simulation.SimulationEventManager
speciesInitiator - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
speciesMade - Variable in class etomica.chem.models.ModelChain
speciesMaxIndexChanged(int) - Method in class etomica.simulation.SimulationEventManager
speciesMembrane - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
speciesMembrane - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
speciesMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosis
speciesMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
SpeciesMethane - Class in etomica.AlkaneEH: Species for methane with explicit hydrogen Bond angle = 109.5 -- not exactly, conformation is changed!!!
SpeciesMethane(ISpace) - Constructor for class etomica.AlkaneEH.SpeciesMethane
SpeciesMethane(ISpace, boolean) - Constructor for class etomica.AlkaneEH.SpeciesMethane
SpeciesMethane - Class in etomica.virial: Species for methane with explicit hydrogen Bond angle = 109.5
SpeciesMethane(ISpace) - Constructor for class etomica.virial.SpeciesMethane
SpeciesMethane(ISpace, boolean) - Constructor for class etomica.virial.SpeciesMethane
speciesMethanol - Static variable in class etomica.models.rowley.DimerApproach
SpeciesMethanol - Class in etomica.models.rowley: Species for methanol with satellite site (Rowley et al 2006).
SpeciesMethanol(ISpace, boolean) - Constructor for class etomica.models.rowley.SpeciesMethanol
SpeciesMethanol - Class in etomica.models.traPPE: Species for methanol with satellite site (Rowley et al 2006).
SpeciesMethanol(ISpace) - Constructor for class etomica.models.traPPE.SpeciesMethanol
speciesMolecules - Variable in class etomica.modules.sam.ConfigurationSAM
speciesMonomer - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
speciesMonomer - Variable in class etomica.modules.colloid.NeighborListManagerColloid
SpeciesN2 - Class in etomica.models.nitrogen: Species nitrogen molecule with 4-points charges
SpeciesN2(ISpace) - Constructor for class etomica.models.nitrogen.SpeciesN2
SpeciesN2(ISpace, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2
SpeciesN2B - Class in etomica.models.nitrogen: Species nitrogen molecule with 4-points charges
SpeciesN2B(ISpace) - Constructor for class etomica.models.nitrogen.SpeciesN2B
SpeciesN2B(ISpace, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2B
SpeciesN2ShellModel - Class in etomica.models.nitrogen: Species nitrogen molecule (shell model) Reference: Fabianski R.
SpeciesN2ShellModel(ISpace) - Constructor for class etomica.models.nitrogen.SpeciesN2ShellModel
SpeciesN2ShellModel(ISpace, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2ShellModel
speciesO - Variable in class etomica.modules.catalysis.Catalysis
speciesO - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
speciesO - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
speciesO - Variable in class etomica.modules.catalysis.MeterDensityO2
SpeciesOriented - Class in etomica.species: Atom type for a rigid molecule with an orientation and (therefore) a moment of inertia.
SpeciesOriented(ISpace) - Constructor for class etomica.species.SpeciesOriented
SpeciesParacetamol - Class in etomica.paracetamol
SpeciesParacetamol(ISpace, boolean) - Constructor for class etomica.paracetamol.SpeciesParacetamol
SpeciesPh3site464 - Class in etomica.virial: Species Phenanthrene molecule rigid , LJ potential, no charge, 3 site model.each benzene ring is a site, 464 model reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
SpeciesPh3site464(ISpace) - Constructor for class etomica.virial.SpeciesPh3site464
SpeciesPh3site464(ISpace, boolean) - Constructor for class etomica.virial.SpeciesPh3site464
SpeciesPh3site545 - Class in etomica.virial: Species Phenanthrene molecule rigid , LJ potential, no charge, 3 site model.each benzene ring is a site reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
SpeciesPh3site545(ISpace) - Constructor for class etomica.virial.SpeciesPh3site545
SpeciesPh3site545(ISpace, boolean) - Constructor for class etomica.virial.SpeciesPh3site545
SpeciesPolyhedron - Class in etomica.species: Species in which molecules are made of a single atom of type SpheroPolyhedron
SpeciesPolyhedron(Simulation, ISpace, List<IVector>, double) - Constructor for class etomica.species.SpeciesPolyhedron
SpeciesPolyhedron(ISpace, List<IVector>, double, IElement) - Constructor for class etomica.species.SpeciesPolyhedron
speciesPotentialIterator - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
speciesRemoved(ISpecies) - Method in class etomica.simulation.SimulationEventManager
speciesSodium - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
speciesSolute - Variable in class etomica.modules.osmosis.OsmosisSim
speciesSolute - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
speciesSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosis
speciesSolute1 - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
speciesSolute2 - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
speciesSolvent - Variable in class etomica.modules.osmosis.OsmosisSim
speciesSolvent - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
speciesSolvent - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
speciesSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosis
speciesSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
speciesSpheres - Variable in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
SpeciesSpheres - Class in etomica.species: Species in which molecules are made of arbitrary number of spheres, with each sphere having the same mass and size (same type).
SpeciesSpheres(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheres
SpeciesSpheres(Simulation, ISpace, int) - Constructor for class etomica.species.SpeciesSpheres
SpeciesSpheres(ISpace, int, IElement) - Constructor for class etomica.species.SpeciesSpheres
SpeciesSpheres(int, IElement, IConformation, ISpace) - Constructor for class etomica.species.SpeciesSpheres
SpeciesSpheres(ISpace, int, IAtomType, IConformation) - Constructor for class etomica.species.SpeciesSpheres
SpeciesSpheresCustom - Class in etomica.species: Species in which molecules are made of arbitrary number of spheres, each of a specified type.
SpeciesSpheresCustom(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresCustom: Constructs instance with 0 components and total number of children equal to 1.
SpeciesSpheresCustom(Simulation, ISpace, int) - Constructor for class etomica.species.SpeciesSpheresCustom: Constructs instance with the given number of atom types.
SpeciesSpheresCustom(ISpace, IElement[]) - Constructor for class etomica.species.SpeciesSpheresCustom: Constructs instance with the given elements.
SpeciesSpheresCustom(ISpace, IAtomType[]) - Constructor for class etomica.species.SpeciesSpheresCustom: Constructs instance with the given atom types.
SpeciesSpheresHetero - Class in etomica.species: Species in which molecules are made of arbitrary number of atoms, with each atom have a given atom type.
SpeciesSpheresHetero(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresHetero: Constructs instance with 0 components and total number of children equal to 1.
SpeciesSpheresHetero(Simulation, ISpace, int) - Constructor for class etomica.species.SpeciesSpheresHetero: Constructs instance with the given number of atom types.
SpeciesSpheresHetero(ISpace, IElement[]) - Constructor for class etomica.species.SpeciesSpheresHetero: Constructs instance with the given elements.
SpeciesSpheresHetero(ISpace, IAtomType[]) - Constructor for class etomica.species.SpeciesSpheresHetero: Constructs instance with the given atom types.
SpeciesSpheresMono - Class in etomica.species: Species in which molecules are each made of a single spherical atom.
SpeciesSpheresMono(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresMono: Constructs instance with a default element
SpeciesSpheresMono(ISpace, IElement) - Constructor for class etomica.species.SpeciesSpheresMono
SpeciesSpheresMono(ISpace, IAtomType) - Constructor for class etomica.species.SpeciesSpheresMono
SpeciesSpheresRotating - Class in etomica.species: Species in which molecules are made of a single atom of type OrientedSphere
SpeciesSpheresRotating(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresRotating
SpeciesSpheresRotating(ISpace, IElement) - Constructor for class etomica.species.SpeciesSpheresRotating
SpeciesSpheresRotatingMolecule - Class in etomica.species: Species in which molecules are made of a single atom.
SpeciesSpheresRotatingMolecule(Simulation, ISpace) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
SpeciesSpheresRotatingMolecule(Simulation, ISpace, IVector) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
SpeciesSpheresRotatingMolecule(ISpace, IAtomType, IVector) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
speciesSurface - Variable in class etomica.modules.catalysis.Catalysis
speciesSurface - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
speciesSurface - Variable in class etomica.modules.catalysis.InteractionTracker
speciesSurface - Variable in class etomica.modules.sam.ConfigurationSAM
speciesSurface - Variable in class etomica.modules.sam.Sam
speciesTopWall - Variable in class etomica.interfacial.LJMC
speciesTopWall - Variable in class etomica.interfacial.LJMD
SpeciesTraPPEAnthracene - Class in etomica.virial: Species Anthracene molecule this is for TraPPE, the Anthracene is rigid , LJ potential, 10 interaction site reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann modified from Species Anthracene molecule class
SpeciesTraPPEAnthracene(ISpace) - Constructor for class etomica.virial.SpeciesTraPPEAnthracene
SpeciesTraPPEAnthracene(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPEAnthracene
SpeciesTraPPECO2 - Class in etomica.virial: Species CO2 molecule this is for TraPPE, the CO2 is rigid , LJ potential + QQ
SpeciesTraPPECO2(ISpace) - Constructor for class etomica.virial.SpeciesTraPPECO2
SpeciesTraPPECO2(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPECO2
SpeciesTraPPENaphthalene - Class in etomica.virial: Species Naphthalene molecule this is for TraPPE, the Naphthalene is rigid , LJ potential reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
SpeciesTraPPENaphthalene(ISpace) - Constructor for class etomica.virial.SpeciesTraPPENaphthalene
SpeciesTraPPENaphthalene(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPENaphthalene
SpeciesTraPPEPhenanthrene - Class in etomica.virial: Species Phenanthrene molecule this is for TraPPE, the Phenanthrene is rigid , LJ potential reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann modified from species of phenanthrene C14H10
SpeciesTraPPEPhenanthrene(ISpace) - Constructor for class etomica.virial.SpeciesTraPPEPhenanthrene
SpeciesTraPPEPhenanthrene(ISpace, boolean) - Constructor for class etomica.virial.SpeciesTraPPEPhenanthrene
speciesTube - Variable in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
speciesTube - Variable in class etomica.modules.dcvgcmd.DCVGCMD
SpeciesTube - Class in etomica.modules.dcvgcmd
SpeciesTube(int, int, ISpace) - Constructor for class etomica.modules.dcvgcmd.SpeciesTube
SpeciesWater3P - Class in etomica.models.water: Species for 3-point water molecule.
SpeciesWater3P(ISpace) - Constructor for class etomica.models.water.SpeciesWater3P
SpeciesWater3P(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater3P
SpeciesWater3POriented - Class in etomica.models.water
SpeciesWater3POriented(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater3POriented
SpeciesWater4P - Class in etomica.models.water: Species for 4-point water molecule.
SpeciesWater4P(ISpace) - Constructor for class etomica.models.water.SpeciesWater4P
SpeciesWater4P(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater4P
SpeciesWater4PCOM - Class in etomica.models.water: Species for 4-point water molecule.
SpeciesWater4PCOM(ISpace) - Constructor for class etomica.models.water.SpeciesWater4PCOM
SpeciesWater4PCOM(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater4PCOM
SpeciesWater4POriented - Class in etomica.models.water
SpeciesWater4POriented(ISpace, boolean) - Constructor for class etomica.models.water.SpeciesWater4POriented
specular - Static variable in class org.jmol.script.Token
specularexponent - Static variable in class org.jmol.script.Token
specularExponent - Static variable in class org.jmol.util.Shader
specularFactor - Static variable in class org.jmol.util.Shader
specularOn - Static variable in class org.jmol.util.Shader
specularpercent - Static variable in class org.jmol.script.Token
specularPercent - Static variable in class org.jmol.util.Shader
specularpower - Static variable in class org.jmol.script.Token
specularPower - Static variable in class org.jmol.util.Shader
Sphere - Class in etomica.math.geometry: A sphere in 3D.
Sphere() - Constructor for class etomica.math.geometry.Sphere: Creates sphere with unit radius
Sphere(double) - Constructor for class etomica.math.geometry.Sphere: Creates sphere of the given radius.
sphere - Static variable in class org.jmol.script.Token
sphereArea(double) - Method in interface etomica.space.ISpace: Returns the surface "area" of the "sphere" defined in the D-dimensional space.
sphereArea(double) - Method in class etomica.space.Space
sphereArea(double) - Method in class etomica.space1d.Space1D
sphereArea(double) - Method in class etomica.space2d.Space2D: Returns 2 PI r.
sphereArea(double) - Method in class etomica.space3d.Space3D
sphereMean(Quaternion[], float[], float) - Static method in class org.jmol.util.Quaternion
SphereRenderer - Class in org.jmol.g3d: Implements high performance rendering of shaded spheres.
sphereShadeIndexes - Static variable in class org.jmol.util.Shader
sphereShadingCalculated - Static variable in class org.jmol.util.Shader
sphereShapeCache - Static variable in class org.jmol.util.Shader
sphereVolume(double) - Method in interface etomica.space.ISpace: Returns the "volume" of the "sphere" defined in the D-dimensional space.
sphereVolume(double) - Method in class etomica.space.Space
sphereVolume(double) - Method in class etomica.space1d.Space1D
sphereVolume(double) - Method in class etomica.space2d.Space2D: Returns PI r^2.
sphereVolume(double) - Method in class etomica.space3d.Space3D
SphericalHarmonics - Class in etomica.math
SphericalHarmonics() - Constructor for class etomica.math.SphericalHarmonics
spiffiness - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
spine - Static variable in class org.jmol.script.Token
spinfps - Static variable in class org.jmol.script.Token
spinner - Variable in class etomica.graphics.DeviceSpinner: Actual JSpinner
SpinnerListener() - Constructor for class etomica.graphics.DeviceSpinner.SpinnerListener
spinnerModel - Variable in class etomica.graphics.DeviceSpinner: Actual spinner model
spins - Variable in class etomica.spin.Heisenberg
spinx - Static variable in class org.jmol.script.Token
spiny - Static variable in class org.jmol.script.Token
spinz - Static variable in class org.jmol.script.Token
spline - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
spline(double[], double, double) - Static method in class etomica.potential.P2O2Bartolomei
spline - Variable in class etomica.virial.overlap.DataVirialOverlap
splineC10 - Variable in class etomica.potential.P2QChemInterpolated
splineC6 - Variable in class etomica.potential.P2QChemInterpolated
splineC8 - Variable in class etomica.potential.P2QChemInterpolated
splineRatio - Variable in class etomica.potential.P2QChemInterpolated
splineRc - Variable in class etomica.potential.P2QChemInterpolated
splineUSCF - Variable in class etomica.potential.P2QChemInterpolated
splint(double[], double[], double) - Static method in class etomica.potential.P2O2Bartolomei
Split - Class in etomica.graph.operations
Split() - Constructor for class etomica.graph.operations.Split
split(String, char) - Static method in class org.jmol.util.TextFormat
splitChars(String, String) - Static method in class org.jmol.util.TextFormat: proper splitting, even for Java 1.3 -- if the text ends in the run, no new line is appended.
SplitGraph - Class in etomica.graph.operations: Split a disconnected graph into multiple graphs.
SplitGraph() - Constructor for class etomica.graph.operations.SplitGraph
splitGrapher - Variable in class etomica.graph.operations.ComponentSubst
SplitOne - Class in etomica.graph.operations: Performs the substitution 1=a+b.
SplitOne() - Constructor for class etomica.graph.operations.SplitOne
SplitOne.SplitOneParameters - Class in etomica.graph.operations
splitOneBC - Variable in class etomica.virial.PYGenerator.IteratorEF
SplitOneBiconnected - Class in etomica.graph.operations: Performs the substitution 1=a+b within each biconnected component.
SplitOneBiconnected() - Constructor for class etomica.graph.operations.SplitOneBiconnected
SplitOneBiconnected.SplitOneParametersBC - Class in etomica.graph.operations
SplitOneParameters(char, char) - Constructor for class etomica.graph.operations.SplitOne.SplitOneParameters
splitOneParameters - Variable in class etomica.virial.PYGenerator.IteratorEF
SplitOneParametersBC(char, char, char) - Constructor for class etomica.graph.operations.SplitOneBiconnected.SplitOneParametersBC
SplitParameters - Class in etomica.graph.operations
SplitParameters(char, char, char) - Constructor for class etomica.graph.operations.SplitParameters
SplitParameters(char, char, char, Property) - Constructor for class etomica.graph.operations.SplitParameters
splitSets(Set<Graph>, int) - Method in class etomica.graph.operations.DecorateWertheim3SiteRho
splitter - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
splitter - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
splitterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
splitterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
spring - Variable in class etomica.interfacial.LJMD.LJMDParams
spring - Variable in class etomica.interfacial.P1Wall
spring - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
spring - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
spring - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
spring - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
spring - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
spring - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
springPosition - Variable in class etomica.interfacial.LJMD.LJMDParams
springPosition - Variable in class etomica.interfacial.P1Wall
sprintf(String, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
sprintf(String, String, Object[]) - Static method in class org.jmol.util.TextFormat: sprintf emulation uses (almost) c++ standard string formats 's' string 'i' or 'd' integer 'f' float/decimal 'p' point3f 'q' quaternion/plane/axisangle ' with added "i" in addition to the insipid "d" (digits?)
sprintfArray(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable: sprintf accepts arguments from the format() function First argument is a format string.
sqdt - Variable in class etomica.modules.rheology.IntegratorPolymer
sqr(double) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
sqr() - Method in class etomica.veos.bigdecimal.BigSurd: Compute the square.
sqr() - Method in class etomica.veos.bigdecimal.BigSurdVec: Compute the square.
sqrt() - Method in class etomica.math.Complex: Complex square root (doesn't change this complex number).
Sqrt() - Constructor for class etomica.util.Function.Sqrt
sqrt(BigDecimal, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The square root.
sqrt(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The square root.
sqrt2 - Variable in class etomica.statmech.HardSphere
sqrt2 - Static variable in class etomica.statmech.HardSphereSolid
sqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
sqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
sqrt3ofhalfofthebondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
sqrtCOtau - Variable in class etomica.models.co2.PNCO2GCPM
sqrtHMsigmas - Variable in class etomica.models.water.PNWaterGCPM
sqrtPI - Variable in class etomica.potential.EwaldSummation
sqrtPiCCtau - Variable in class etomica.models.co2.PNCO2GCPM
sqrtPiCOtau - Variable in class etomica.models.co2.PNCO2GCPM
sqrtPiHMsigmas - Variable in class etomica.models.water.PNWaterGCPM
sqrtPiMMsigmas - Variable in class etomica.models.water.PNWaterGCPM
sqrtSimOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
sqrtSimOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
sqrtTemperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
sqrtWVC - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
sqrtWVC - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
Square - Class in etomica.math.geometry: A 2-dimensional geometric square.
Square(ISpace) - Constructor for class etomica.math.geometry.Square: Constructs a square of unit size.
Square(ISpace, double) - Constructor for class etomica.math.geometry.Square: Constructs a square with edge length having the given value.
squared() - Method in interface etomica.api.IVector: Returns the square magnitude of this vector, e.g., x^2 + y^2 for D = 2.
squared() - Method in class etomica.space1d.Vector1D
squared() - Method in class etomica.space2d.Vector2D
squared() - Method in class etomica.space3d.Vector3D
squared() - Method in class etomica.spaceNd.VectorND
sqv - Variable in class etomica.potential.P2SpheroPolyhedron
ss - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
ss - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
ss - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
ss - Variable in class etomica.normalmode.SimLJVacancy.LJParams
ss - Variable in class etomica.util.numerical.AkimaSplineSmoother
ssbond - Static variable in class org.jmol.script.Token
ssbondsbackbone - Static variable in class org.jmol.script.Token
ssInit - Variable in class etomica.util.numerical.AkimaSplineSmootherDy
Standard - Class in etomica.virial.cluster
STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverage
STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverageBlockless
STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
standardDeviation - Variable in class etomica.data.AccumulatorAverage
standardDeviation - Variable in class etomica.data.AccumulatorAverageBlockless
standardLensPoint - Variable in class etomica.virial.MCMoveClusterAtomHSRing
standardLevel - Static variable in class org.jmol.util.Geodesic: 3 levels, 0 through 3
star - Static variable in class org.jmol.script.Token
START - Static variable in class etomica.action.activity.ControllerEvent
start() - Method in class etomica.graph.iterators.ChainedIterator
START - Static variable in class etomica.util.Debug: what step of the integrator debugging should start from.
start - Variable in class g3dsys.images.Line
START_ACTION - Static variable in class etomica.action.activity.ControllerEvent
START_URGENT_ACTION - Static variable in class etomica.action.activity.ControllerEvent
startAtom - Variable in class etomica.threaded.atom.PotentialMasterListWorker
startAtom - Variable in class etomica.virial.MCMoveClusterAtomMulti
startAtom0 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
startAtom1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
startBeadHalfs - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
starter - Variable in class etomica.modules.clustergenerator.MyApplet
Starter() - Constructor for class etomica.modules.clustergenerator.MyApplet.Starter
startMolecule - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
startOrtho - Variable in class etomica.dimer.IntegratorDimerRT
startRotate(float, float) - Method in class etomica.graphics.DisplayCanvas
startRotation(int, int) - Method in class g3dsys.control.G3DSys
startTimer(String) - Static method in class org.jmol.util.Logger
startWithDim(Dimension) - Method in class etomica.units.UnitGraphics
statChoices() - Static method in class etomica.data.AccumulatorAverage
statChoices() - Static method in class etomica.data.AccumulatorAverageBlockless
statChoices() - Static method in class etomica.data.AccumulatorAverageBlocklessSlim
statChoices() - Static method in class etomica.data.AccumulatorAverageCovariance
statChoices() - Static method in class etomica.data.AccumulatorRatioAverage
Statcoulomb - Class in etomica.units: The statcoulomb unit of electrical charge, which is the standard unit of charge in the CGS unit system.
state(int) - Method in interface etomica.tmmc.MacrostateManager: Returns the value of the macrostate variable corresponding to the given index.
stateChanged(ChangeEvent) - Method in class etomica.graphics.DeviceBox: calls doUpdate method.
stateChanged(ChangeEvent) - Method in class etomica.graphics.DeviceSpinner.SpinnerListener
stateChanged(ChangeEvent) - Method in class etomica.graphics.DisplayTextBox: calls doUpdate method.
stateIndex(IBox) - Method in interface etomica.tmmc.MacrostateManager: Returns an index identifying the current macrostate occupied by the box.
stateUpDown - Variable in class etomica.atom.iterator.TripletInnerSequential
StaticConstants - Class in org.jmol.constant
StaticConstants() - Constructor for class org.jmol.constant.StaticConstants
StatType(String, int) - Constructor for class etomica.data.AccumulatorAverage.StatType
StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageBlockless.StatType
StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageBlocklessSlim.StatType
status(byte) - Method in class etomica.graph.traversal.AbstractTraversal
STATUS_ARTICULATION_POINT - Static variable in interface etomica.graph.traversal.Traversal
STATUS_START_BICOMPONENT - Static variable in interface etomica.graph.traversal.Traversal
STATUS_START_COMPONENT - Static variable in interface etomica.graph.traversal.Traversal
STATUS_VISITED_ALL - Static variable in interface etomica.graph.traversal.Traversal
STATUS_VISITED_BICOMPONENT - Static variable in interface etomica.graph.traversal.Traversal
STATUS_VISITED_COMPONENT - Static variable in interface etomica.graph.traversal.Traversal
STATUS_VISITED_NODE - Static variable in interface etomica.graph.traversal.Traversal
statusreporting - Static variable in class org.jmol.script.Token
stddev - Static variable in class org.jmol.script.Token
stdev - Variable in class etomica.data.AccumulatorAverageCollapsingLog
STDEV - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
STDEV - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
STDEV2 - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
SteepestDescent - Class in etomica.conjugategradient
SteepestDescent(Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.SteepestDescent
SteepestDescent - Class in etomica.util.numerical
SteepestDescent(FunctionMultiDimensionalDifferentiable) - Constructor for class etomica.util.numerical.SteepestDescent
steepestDescentAlgorithm() - Method in class etomica.conjugategradient.SteepestDescent: Steepest Descent solution for Ax = b
stepCount - Variable in class etomica.action.ActionIntegrate
stepCount - Variable in class etomica.action.activity.ActivityIntegrate
stepCount - Variable in class etomica.data.DataPumpListenerPow
stepCount - Variable in class etomica.integrator.Integrator
stepCount - Static variable in class etomica.util.Debug: Provides step count to other pieces of code that want to know the step count.
stepFactor - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
stepFinished() - Method in class etomica.integrator.IntegratorEventManager
stepFrac - Variable in class etomica.overlap.IntegratorOverlap
stepLength - Variable in class etomica.dimer.IntegratorDimerMin
steps - Variable in class etomica.AlkaneEH.CH4NVT.Param
steps - Variable in class etomica.AlkaneEH.DHS_NVT.Param
steps - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
steps - Variable in class etomica.dielectric.DHS_NVT.Param
steps - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
steps - Variable in class etomica.dielectric.TIP4P_NVT.Param
steps - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
steps - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
steps - Variable in class etomica.interfacial.LJMC.LjMC3DParams
steps - Variable in class etomica.interfacial.LJMD.LJMDParams
steps - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
steps - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
steps - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
steps - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
steps - Variable in class etomica.normalmode.SimLJVacancy.LJParams
steps - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
steps - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
stepSize - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
stepSize - Variable in class etomica.integrator.mcmove.MCMoveStep
stepSizeMax - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
stepSizeMax - Variable in class etomica.integrator.mcmove.MCMoveStep
stepSizeMin - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
stepSizeMin - Variable in class etomica.integrator.mcmove.MCMoveStep
stepsPerBlock - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
stepsPerBlock - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
stepStarted() - Method in class etomica.integrator.IntegratorEventManager
stereodegrees - Static variable in class org.jmol.script.Token
stillOnPolymer0 - Variable in class etomica.atom.iterator.ANIntergroupExchange
stokeslet(double) - Method in class etomica.modules.droplet.IntegratorDroplet
STOP - Static variable in class etomica.util.Debug: what step of the integrator should the simulation bail set this to prevent Etomica from running for a long time while outputting debugging information (potentially filling up the disk)
stopAtom - Variable in class etomica.threaded.atom.PotentialMasterListWorker
stopNow - Variable in class etomica.modules.clustergenerator.MyApplet
STOPPED - Static variable in class etomica.action.activity.Controller.ActionStatus
stopper - Variable in class etomica.modules.clustergenerator.MyApplet
Stopper() - Constructor for class etomica.modules.clustergenerator.MyApplet.Stopper
stopRotate() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
stopRotate() - Method in class etomica.graphics.DisplayCanvas
stopRotate() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
stopRotation() - Method in class g3dsys.control.G3DSys
stopSimulation - Variable in class etomica.virial.GUI.models.ModelSimulationEnvironment
storeAngularMomentum - Variable in class etomica.integrator.IntegratorRigidIterative
StoredIterator - Class in etomica.graph.iterators
StoredIterator(byte) - Constructor for class etomica.graph.iterators.StoredIterator
straightness - Static variable in class org.jmol.script.Token
StrainColorScheme - Class in etomica.modules.materialfracture
StrainColorScheme() - Constructor for class etomica.modules.materialfracture.StrainColorScheme
strandcount - Static variable in class org.jmol.script.Token
strandcountformeshribbon - Static variable in class org.jmol.script.Token
strandcountforstrands - Static variable in class org.jmol.script.Token
strands - Variable in class etomica.graph.property.FFTDecomposition
strands - Variable in class etomica.graph.property.IsFFT
strands - Static variable in class org.jmol.script.Token
streamOut(OutputStream) - Method in class etomica.graph.viewer.GraphMap
STRING - Static variable in class etomica.graphics.DeviceBox.LabelType
STRING - Static variable in class etomica.graphics.DisplayTextBox.LabelType
string - Static variable in class org.jmol.script.Token
stringBuilder - Variable in class etomica.graphics.DisplayTable
StringFeature - Class in etomica.compatibility
StringFeature(String, String) - Constructor for class etomica.compatibility.StringFeature
stringiWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
stringOmega2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
Strings - Class in etomica.util: Non-instantiable class providing a few static methods for String manipulation.
stringToDim(String) - Static method in class etomica.units.UnitFilter
stringToUnit(String) - Static method in class etomica.units.UnitFilter
stringToUnitSystem(String) - Static method in class etomica.units.UnitFilter
stringWidth(String) - Method in class org.jmol.util.JmolFont
stringWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
stringWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
StringXBuilder - Class in org.jmol.util: Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
StringXBuilder() - Constructor for class org.jmol.util.StringXBuilder
strparam - Static variable in class org.jmol.script.Token
strproperty - Static variable in class org.jmol.script.Token
strucid - Static variable in class org.jmol.script.Token
strucno - Static variable in class org.jmol.script.Token
struct - Variable in class etomica.data.meter.MeterStructureFactor
structure - Static variable in class org.jmol.script.Token
strutdefaultradius - Static variable in class org.jmol.script.Token
strutlengthmaximum - Static variable in class org.jmol.script.Token
struts - Static variable in class org.jmol.script.Token
strutsmultiple - Static variable in class org.jmol.script.Token
strutspacing - Static variable in class org.jmol.script.Token
Stuff(PotentialGroup, PotentialGroup, ISpecies) - Constructor for class etomica.parser.ParserLAMMPS.Stuff
stx3leval(double, double, double) - Static method in class etomica.potential.P2O2Bartolomei
sType - Variable in class etomica.virial.Species7SiteRigidSF6
Sub - Class in etomica.graph.operations
Sub() - Constructor for class etomica.graph.operations.Sub
sub(Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
sub(Matrix4f) - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
sub(Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1).
sub2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f: Sets the value of this tuple to the vector difference of tuple t1 and t2 (this = t1 - t2).
subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
subBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
subBox - Variable in class etomica.metastable.MeterDensityDistribution
subClusterValues - Variable in class etomica.virial.ClusterSumIC
subCriterion - Variable in class etomica.nbr.CriterionAdapter
subCriterion - Variable in class etomica.nbr.molecule.CriterionAdapterMolecular
subData - Variable in class etomica.metastable.MeterDensityDistribution
subDataInfo - Variable in class etomica.data.types.DataGroup.DataInfoGroup
subDataInfo - Variable in class etomica.data.types.DataGroup.DataInfoGroupFactory
subIntegrator - Variable in class etomica.thermointegration.IntegratorThermodynamic
subst - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
subst - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
substMinMulti(Graph) - Method in class etomica.virial.cluster.VirialDiagrams
substring(int) - Method in class org.jmol.util.StringXBuilder
substring2(int, int) - Method in class org.jmol.util.StringXBuilder
substructure - Static variable in class org.jmol.script.Token
substSet - Variable in class etomica.virial.PYGenerator.IteratorEF
subtract(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Subtract another polynomial
subtract(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec: Subtract another number.
subtract(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec: Subtract another number.
subtract(Rational) - Method in class etomica.veos.bigdecimal.Rational: Subtract another fraction.
subtract(BigInteger) - Method in class etomica.veos.bigdecimal.Rational: Subtract an integer.
subtract(int) - Method in class etomica.veos.bigdecimal.Rational: Subtract an integer.
subtractApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
subtractApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
subtractApprox - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
subtractApprox - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
subtractApprox - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
subtractApprox - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
subtractApprox - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
subtractHalf - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
subtractHalf - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
subtractHalf - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
subtractRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Subtract and round according to the larger of the two ulp's.
subtractRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Subtract and round according to the larger of the two ulp's.
subtractWhat - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
subtractWhat - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
Sulfur - Class in etomica.chem.elements: Class for the Sulfur element.
Sulfur(String) - Constructor for class etomica.chem.elements.Sulfur
Sulfur(String, double) - Constructor for class etomica.chem.elements.Sulfur
sulfurType - Variable in class etomica.modules.sam.IntegratorVelocityVerletSAM
sum - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
sum - Variable in class etomica.data.AccumulatorAverageBlockless
sum - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
sum - Variable in class etomica.data.AccumulatorAverageFixed
sum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
Sum - Class in etomica.graph.operations
Sum() - Constructor for class etomica.graph.operations.Sum
sum - Variable in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
sum - Variable in class etomica.mappedvirial.MappedUpotential
sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
sum - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
sum - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
sum() - Method in class etomica.potential.EwaldSumMolecules
sum - Variable in class etomica.potential.PotentialCalculationEnergySum
sum - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
sum - Variable in class etomica.util.HistogramSimple
sum(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Generates the set of diagrams obtained by adding the second set to the first set.
sum - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
sum - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
sum - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
sum - Static variable in class org.jmol.script.Token
sum1 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
sum1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
sum1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
sum2 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
sum2 - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
sum2 - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
sum2 - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
sum2 - Static variable in class org.jmol.script.Token
sumBlockSquare - Variable in class etomica.data.AccumulatorAverageFixed
sumBlockSquare - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
sumCheck - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
sumDelete - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
sumInsert - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
summary(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
summer - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
summer - Variable in class etomica.normalmode.NormalModesMolecular
sums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
sums - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
sums - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
sums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoffLS
sums - Variable in class etomica.util.HistogramNotSoSimple
sums - Variable in class etomica.util.HistogramReweightedData
sumSqD2 - Variable in class etomica.util.numerical.AkimaSplineSmoother
sumSqD2D - Variable in class etomica.util.numerical.AkimaSplineSmoother
sumSqD3 - Variable in class etomica.util.numerical.AkimaSplineSmoother
sumSqD3D - Variable in class etomica.util.numerical.AkimaSplineSmoother
sumSqDy - Variable in class etomica.util.numerical.AkimaSplineSmoother
sumSquare - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
sumSquare - Variable in class etomica.data.AccumulatorAverageBlockless
sumSquare - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
sumSquare - Variable in class etomica.data.AccumulatorAverageFixed
sumSquare - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
sumWeights - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
SuperImposeGraphs(Graph, Graph) - Static method in class etomica.virial.IEGenerator
support - Variable in class etomica.graphics.Display
suppressAction - Variable in class etomica.graphics.DeviceSlider
suppressMakeAgent - Variable in class etomica.potential.P2SquareWellRobust
surface - Static variable in class org.jmol.script.Token
surfaceColor - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
surfaceCursor - Variable in class etomica.modules.sam.CriterionTether3
surfaceDim - Variable in class etomica.data.DataProcessorInterfacialTension
surfacedistance - Static variable in class org.jmol.script.Token
surfacePosition - Variable in class etomica.modules.sam.SamGraphic.ModifierWallPosition
surfaceSet - Variable in class org.jmol.util.MeshSurface
SurfaceTensionMapped - Class in etomica.surfacetension: DataProcessor that adds in mapped average contributions to the surface tension.
SurfaceTensionMapped(ISpace, IBox, ISpecies, IPotentialMaster) - Constructor for class etomica.surfacetension.SurfaceTensionMapped
surfaceType - Variable in class etomica.modules.sam.CriterionTether3
surfactant - Variable in class etomica.modules.interfacial.InterfacialSW
surfactantProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
surfactantProfilePump - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
sv - Variable in class etomica.potential.P2SpheroPolyhedron
sValue(Token) - Static method in class org.jmol.script.ScriptVariable
SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverter: SVG file extension
SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource: SVG file extension
SVGConverter - Class in etomica.graph.view.rasterizer: This application can be used to convert SVG images to raster images.
SVGConverter() - Constructor for class etomica.graph.view.rasterizer.SVGConverter
SVGConverter(SVGConverterController) - Constructor for class etomica.graph.view.rasterizer.SVGConverter
SVGConverter.SVGFileFilter - Class in etomica.graph.view.rasterizer: Convenience class to filter svg files
SVGConverterController - Interface in etomica.graph.view.rasterizer: Interface for controlling some aspectes of the SVGConverter operation.
SVGConverterDocumentSource - Class in etomica.graph.view.rasterizer
SVGConverterDocumentSource(SVGDocument) - Constructor for class etomica.graph.view.rasterizer.SVGConverterDocumentSource
SVGConverterException - Exception in etomica.graph.view.rasterizer: Describes an error condition in SVGConverter
SVGConverterException(String) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
SVGConverterException(String, Object[]) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
SVGConverterException(String, Object[], boolean) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
SVGConverterException(String, boolean) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
SVGConverterFileSource - Class in etomica.graph.view.rasterizer: Describes a file source for the SVGConverter
SVGConverterFileSource(File) - Constructor for class etomica.graph.view.rasterizer.SVGConverterFileSource
SVGConverterFileSource(File, String) - Constructor for class etomica.graph.view.rasterizer.SVGConverterFileSource
SVGConverterSource - Interface in etomica.graph.view.rasterizer: Interface used to handle both Files and URLs in the SVGConverter
SVGConverterURLSource - Class in etomica.graph.view.rasterizer
SVGConverterURLSource(String) - Constructor for class etomica.graph.view.rasterizer.SVGConverterURLSource
SVGFileFilter() - Constructor for class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
SVGZ_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource
swap(int, int) - Method in class etomica.virial.cluster.ClusterDiagram: Swaps point1 and point2.
swap(Object[], int, int) - Static method in class org.jmol.util.ArrayUtil
swap0n(byte) - Method in class etomica.virial.cluster.VirialDiagrams
swap0n(byte, int, int, boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
swap0n(byte) - Method in class etomica.virial.cluster.VirialDiagramsPT
swapAllAndCompare(boolean, ClusterDiagram, int[]) - Static method in class etomica.virial.cluster.ClusterGenerator
SwapFactory() - Constructor for class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory
SwapFactory() - Constructor for class etomica.virial.paralleltempering.MCMoveSwapCluster.SwapFactory
swapInt(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
swappedBoxes() - Method in interface etomica.integrator.IntegratorPT.MCMoveSwap
swappedBoxes() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration: Implementation of MCMoveSwap interface
swappedBoxes() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster: Implementation of MCMoveSwap interface
sweepRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
switchFac - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
switchFac - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
Swmd - Class in etomica.modules.swmd
Swmd(Space) - Constructor for class etomica.modules.swmd.Swmd
SwMd2D - Class in etomica.simulation.prototypes: Simple square-well molecular dynamics simulation in 2D
SwMd2D() - Constructor for class etomica.simulation.prototypes.SwMd2D
SWMD3D - Class in etomica.simulation.prototypes
SWMD3D(ISpace) - Constructor for class etomica.simulation.prototypes.SWMD3D
SwmdGraphic - Class in etomica.modules.swmd
SwmdGraphic(Swmd, Space) - Constructor for class etomica.modules.swmd.SwmdGraphic
SwmdGraphic.Applet - Class in etomica.modules.swmd
SwmdGraphic.DataSinkExcludeOverlap - Class in etomica.modules.swmd
SwmdGraphic.ModifierAtomDiameter - Class in etomica.modules.swmd
sx1 - Variable in class etomica.dimer.P1LepsHarmonic
sx2 - Variable in class etomica.dimer.P1LepsHarmonic
sy1 - Variable in class etomica.dimer.P1LepsHarmonic
sy2 - Variable in class etomica.dimer.P1LepsHarmonic
symbol - Variable in class etomica.chem.elements.Element
symbol() - Method in class etomica.units.CompoundUnit
symbol() - Method in class etomica.units.Prefix
symbol() - Method in class etomica.units.PrefixedUnit: Accessor for symbol of baseUnit
symbol() - Method in class etomica.units.SimpleUnit: Accessor for symbol of unit
symbol() - Method in class etomica.units.systems.LJ.LJUnit
symbol() - Method in interface etomica.units.Unit: Returns the symbol of unit, such as "g" for grams.
symbol - Static variable in class org.jmol.script.Token
symmetry - Static variable in class org.jmol.script.Token
symop - Static variable in class org.jmol.script.Token
syncmouse - Static variable in class org.jmol.script.Token
syncscript - Static variable in class org.jmol.script.Token
SZ_INT - Static variable in class etomica.graph.traversal.BitmapUtils
SZ_LONG - Static variable in interface etomica.graph.model.Bitmap

T

T - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
T - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
T - Variable in class etomica.interfacial.LJMC.LjMC3DParams
T - Variable in class etomica.interfacial.LJMD.LJMDParams
T - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
T - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
t - Variable in class etomica.util.numerical.AkimaSpline
t - Variable in class etomica.util.numerical.AkimaSplineSmoother
T - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
t - Variable in class etomica.virial.ClusterPY
t1 - Variable in class etomica.meam.ParameterSetMEAM
T1ij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
T1ij - Variable in class etomica.normalmode.PotentialCalculationLJSP
T1ik - Variable in class etomica.normalmode.PotentialCalculationEFSSP
T1RHOj0 - Static variable in class etomica.meam.PotentialMEAM
t2 - Variable in class etomica.meam.ParameterSetMEAM
T2ij - Variable in class etomica.normalmode.PotentialCalculationLJSP
T2RHOj0 - Static variable in class etomica.meam.PotentialMEAM
t3 - Variable in class etomica.meam.ParameterSetMEAM
T3ij - Variable in class etomica.normalmode.PotentialCalculationLJSP
T3RHOj0 - Static variable in class etomica.meam.PotentialMEAM
ta - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
taa - Static variable in class etomica.potential.P2O2Bartolomei
taaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
taaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
TABBED_PANE - Static variable in class etomica.graphics.SimulationGraphic
tabbedPane - Variable in class etomica.graphics.SimulationPanel
tableModel() - Method in class etomica.graphics.DisplayTable
tableRowCountChanged(DataSinkTable) - Method in interface etomica.data.DataTableListener: Method called to indicate that the number of rows in the table has changed.
tableRowCountChanged(DataSinkTable) - Method in class etomica.graphics.DisplayTable: Part of the DataTableListener interface.
tableRowHeadersChanged(DataSinkTable) - Method in interface etomica.data.DataTableListener: Method called to indicate that the row headers in the table have changed.
tableRowHeadersChanged(DataSinkTable) - Method in class etomica.graphics.DisplayTable
tag - Variable in class etomica.data.DataDistributer
tag - Variable in class etomica.data.DataDump
tag - Variable in class etomica.data.DataFork
tag - Variable in class etomica.data.DataGroupSplitter
tag - Variable in class etomica.data.DataProcessor
tag - Variable in class etomica.data.DataSourceFunction
tag - Variable in class etomica.data.DataSourceGroup
tag - Variable in class etomica.data.DataSourceIndependentSimple
tag - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
tag - Variable in class etomica.data.DataSourceRmsVelocity
tag - Variable in class etomica.data.DataSourceScalar
tag - Variable in class etomica.data.DataSourceTensorVirialHard
tag - Variable in class etomica.data.DataSourceUniform
tag - Variable in class etomica.data.DataSplitter
tag - Variable in class etomica.data.HistogramDataSource
tag - Variable in class etomica.data.meter.MeterDihedralAngle
tag - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
tag - Variable in class etomica.data.meter.MeterHyperVirial
tag - Variable in class etomica.data.meter.MeterMomentumCOM
tag - Variable in class etomica.data.meter.MeterPositionCOM
tag - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
tag - Variable in class etomica.data.meter.MeterPressureHardTensor
tag - Variable in class etomica.data.meter.MeterPressureTensor
tag - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
tag - Variable in class etomica.data.meter.MeterProfile
tag - Variable in class etomica.data.meter.MeterProfileByAtoms
tag - Variable in class etomica.data.meter.MeterProfileByVolume
tag - Variable in class etomica.data.meter.MeterRDF
tag - Variable in class etomica.data.meter.MeterRDFPC
tag - Variable in class etomica.data.meter.MeterTensorVelocity
tag - Variable in class etomica.freeenergy.npath.DataSourceEnergies
tag - Variable in class etomica.gaussianwork.MeterBoltzmannA
tag - Variable in class etomica.gaussianwork.MeterBoltzmannB
tag - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
tag - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
tag - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
tag - Variable in class etomica.liquidLJ.MeterPU
tag - Variable in class etomica.liquidLJ.MeterPUCut
tag - Variable in class etomica.liquidLJ.MeterPUCutLS
tag - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
tag - Variable in class etomica.mappedvirial.MeterMeanForce
tag - Variable in class etomica.models.nitrogen.MeterBoltzmann
tag - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
tag - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
tag - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
tag - Variable in class etomica.models.oneDHardRods.MeterNMCBaskets
tag - Variable in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
tag - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
tag - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
tag - Variable in class etomica.modules.chainequilibrium.MeterChainLength
tag - Variable in class etomica.modules.droplet.MeterDeformation
tag - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
tag - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
tag - Variable in class etomica.modules.interfacial.MeterOrientation
tag - Variable in class etomica.modules.mu.DataSourceWallPressureMu
tag - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
tag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
tag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
tag - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
tag - Variable in class etomica.modules.rosmosis.MeterFlux
tag - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
tag - Variable in class etomica.modules.sam.MeterTilt
tag - Variable in class etomica.normalmode.DataSourceFE
tag - Variable in class etomica.normalmode.DataSourceFEHistogram
tag - Variable in class etomica.normalmode.DataSourceImposedFEFit
tag - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
tag - Variable in class etomica.normalmode.DataSourcePMu
tag - Variable in class etomica.normalmode.DataSourcePN
tag - Variable in class etomica.normalmode.MeterBoltzmann
tag - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
tag - Variable in class etomica.normalmode.MeterBoltzmannHTTP
tag - Variable in class etomica.normalmode.MeterBoltzmannTarget
tag - Variable in class etomica.normalmode.MeterDADB
tag - Variable in class etomica.normalmode.MeterDDP
tag - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
tag - Variable in class etomica.normalmode.MeterDirectSamplingTarget
tag - Variable in class etomica.normalmode.MeterDP
tag - Variable in class etomica.normalmode.MeterOverlapSwitch
tag - Variable in class etomica.normalmode.MeterPlaneSlip
tag - Variable in class etomica.normalmode.MeterSamplingHarmonic
tag - Variable in class etomica.normalmode.MeterSamplingTarget
tag - Variable in class etomica.normalmode.MeterSolidDA
tag - Variable in class etomica.normalmode.MeterSolidDACut
tag - Variable in class etomica.normalmode.MeterSolidMirror
tag - Variable in class etomica.normalmode.MeterSolidProps
tag - Variable in class etomica.normalmode.MeterSolidPropsLJ
tag - Variable in class etomica.normalmode.MeterTargetTP
tag - Variable in class etomica.normalmode.MeterTilt
tag - Variable in class etomica.normalmode.MeterTiltHistogram
tag - Variable in class etomica.normalmode.MeterTiltRotation
tag - Variable in class etomica.normalmode.MeterTiltRotationStdev
tag - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
tag - Variable in class etomica.normalmode.MeterWorkBennetTarget
tag - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
tag - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
tag - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
tag - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
tag - Variable in class etomica.normalmode.MeterWorkTargetBennet
tag - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
tag - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
tag - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
tag - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
tag - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
tag - Variable in class etomica.overlap.MeterOverlap
tagged - Variable in class etomica.modules.chainequilibrium.MeterChainLength.AtomTag
tagManager - Variable in class etomica.modules.chainequilibrium.MeterChainLength
tags - Variable in class etomica.data.DataInfoFactory
tags - Variable in class etomica.graphics.DataTagBag
tailType - Variable in class etomica.modules.interfacial.InterfacialSW
tajmols - Static variable in class etomica.potential.P2O2Bartolomei
tajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
tajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
tajp1 - Static variable in class etomica.potential.P2O2Bartolomei
tajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
tajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
tajpn - Static variable in class etomica.potential.P2O2Bartolomei
tajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
tajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
tan() - Method in class etomica.math.Complex: Tangent of this Complex number (doesn't change this Complex number).
tan(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The trigonometric tangent.
tangledMolecules - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
tangledMolecules - Variable in class etomica.virial.MCMoveClusterRingRegrow
tangledMolecules - Variable in class etomica.virial.MCMoveClusterRingScale
tanh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: The hyperbolic tangent.
taperOrder - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
taperOrder - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
target - Variable in class etomica.atom.iterator.ApiIndexList
TARGET - Static variable in class etomica.overlap.DataOverlap
targetAcc - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
targetAccumulator - Variable in class etomica.virial.overlap.DataSourceVirialOverlap
targetAccumulator - Variable in class etomica.virial.overlap.DataVirialOverlap
targetAction - Variable in class etomica.graphics.DeviceButton
targetAction - Variable in class etomica.graphics.DeviceButtonGroup
targetAction - Variable in class etomica.graphics.DeviceSlider
targetAction - Variable in class etomica.graphics.DeviceSpinner
targetAction - Variable in class etomica.zeolite.DeviceButtonSingle
targetAtom - Variable in class etomica.atom.iterator.ApiIntergroup
targetAtom - Variable in class etomica.atom.iterator.TripletInnerSequential
targetAtom - Variable in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
targetAtom - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
targetAvg - Variable in class etomica.overlap.DataOverlap
targetAvg - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
targetCluster - Variable in class etomica.virial.MeterVirialBDBin
targetCluster - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
targetCluster - Variable in class etomica.virial.MeterVirialBinMultiThreaded
targetCluster - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
targetCluster - Variable in class etomica.virial.MeterVirialIC
targetCluster - Variable in class etomica.virial.simulations.ModifierTPI
targetDataInterval - Variable in class etomica.normalmode.SimOverlapModule
targetErr - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
targetIndex - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
targetMolecule - Variable in class etomica.modules.sam.CriterionTether3
targetSum - Variable in class etomica.normalmode.MeterOverlapSwitch
targHist - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
targPiHist - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
targShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
targShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
targShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
tau - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
tau - Variable in class etomica.models.water.P2Water4PSoft
tauAll - Variable in class etomica.models.co2.PNCO2GCPM
tauC - Variable in class etomica.models.co2.PNCO2GCPM
tauO - Variable in class etomica.models.co2.PNCO2GCPM
tav1() - Method in class etomica.meam.PotentialMEAM
tav2() - Method in class etomica.meam.PotentialMEAM
tav3() - Method in class etomica.meam.PotentialMEAM
tb - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
tbet - Static variable in class etomica.potential.P2O2Bartolomei
tbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
tbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
Tc - Static variable in class etomica.modules.adsorption.EOSSW
tCompute(double[][], double[][], int, int, double) - Static method in class etomica.virial.OrnsteinZernike
TE(IVector) - Method in interface etomica.api.IVectorMutable: Times-equals (*=) operation.
TE(double) - Method in interface etomica.api.IVectorMutable: Multiplies all components by a constant.
TE(IData) - Method in interface etomica.data.IData: Times-equals (*=) operation.
TE(double) - Method in interface etomica.data.IData: Times-equals (*=) operation, multiplying all values in data by given value.
TE(IData) - Method in class etomica.data.types.DataDouble: Times-equals (*=) operation.
TE(double) - Method in class etomica.data.types.DataDouble: Times-equals (*=) operation.
TE(IData) - Method in class etomica.data.types.DataDoubleArray: Times-equals (*=) operation.
TE(double) - Method in class etomica.data.types.DataDoubleArray: Times-equals (*=) operation.
TE(IData) - Method in class etomica.data.types.DataDoubleBDArray: Times-equals (*=) operation.
TE(double) - Method in class etomica.data.types.DataDoubleBDArray: Times-equals (*=) operation.
TE(IData) - Method in class etomica.data.types.DataGroup
TE(double) - Method in class etomica.data.types.DataGroup
TE(IData) - Method in class etomica.data.types.DataTensor: Times-equals (*=) operation.
TE(double) - Method in class etomica.data.types.DataTensor: Times-equals (*=) operation.
TE(IData) - Method in class etomica.data.types.DataVector: Times-equals (*=) operation.
TE(double) - Method in class etomica.data.types.DataVector: Times-equals (*=) operation.
TE(double) - Method in class etomica.math.Quaternion: Multiplies all the components of the Quaternion q by the given scalar
TE(double) - Method in interface etomica.space.Tensor
TE(Tensor) - Method in interface etomica.space.Tensor
TE(double) - Method in class etomica.space1d.Tensor1D
TE(Tensor) - Method in class etomica.space1d.Tensor1D
TE(double) - Method in class etomica.space1d.Vector1D
TE(IVector) - Method in class etomica.space1d.Vector1D
TE(double) - Method in class etomica.space2d.Tensor2D
TE(Tensor) - Method in class etomica.space2d.Tensor2D
TE(double) - Method in class etomica.space2d.Vector2D
TE(IVector) - Method in class etomica.space2d.Vector2D
TE(double) - Method in class etomica.space3d.Tensor3D
TE(Tensor) - Method in class etomica.space3d.Tensor3D
TE(double) - Method in class etomica.space3d.Vector3D
TE(IVector) - Method in class etomica.space3d.Vector3D
TE(double) - Method in class etomica.spaceNd.TensorND
TE(Tensor) - Method in class etomica.spaceNd.TensorND
TE(double) - Method in class etomica.spaceNd.VectorND
TE(IVector) - Method in class etomica.spaceNd.VectorND
TE(IBigValue) - Method in class etomica.veos.BigValue: Times-equals (*=) operation.
TE(double) - Method in class etomica.veos.BigValue: Times-equals (*=).
TE(IBigValue) - Method in interface etomica.veos.IBigValue: Times-equals (*=) operation.
TE(double) - Method in interface etomica.veos.IBigValue: Times-equals (*=).
TE(IBigValue) - Method in class etomica.veos.MyBigDecimal: Times-equals (*=) operation.
TE(double) - Method in class etomica.veos.MyBigDecimal: Times-equals (*=).
TEAL - Static variable in class org.jmol.util.Colix
TEln(double) - Method in class etomica.veos.BigValue: Times-equals (*=) operation, multiplying by a value given as its logarithm.
temp - Variable in class etomica.integrator.IntegratorVelocityVerletShake
temp - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
temp - Variable in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
temp - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
temp - Variable in class etomica.space3d.Orientation3D
temp2 - Variable in class etomica.space3d.Orientation3D
tempAngularVelocity - Variable in class etomica.integrator.IntegratorRigidIterative
tempAngularVelocity - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
tempAxesTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
temperature - Variable in class etomica.action.BoxQuench
temperature - Variable in class etomica.action.BoxRandomizeMomenta
temperature - Variable in class etomica.action.BoxScaleMomenta
temperature - Variable in class etomica.AlkaneEH.DHS_NVT.Param
temperature - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
temperature - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
temperature - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
temperature - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
temperature - Variable in class etomica.data.meter.MeterHyperVirial
temperature - Variable in class etomica.data.meter.MeterPressure
temperature - Variable in class etomica.data.meter.MeterWidomInsertion
temperature - Variable in class etomica.dielectric.DHS_NVT.Param
temperature - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
temperature - Variable in class etomica.gaussianwork.MeterBoltzmannA
temperature - Variable in class etomica.gaussianwork.MeterBoltzmannB
temperature - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
temperature - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
temperature - Variable in class etomica.integrator.IntegratorBox
temperature - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
temperature - Variable in class etomica.integrator.mcmove.MCMoveVolume
temperature - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
temperature - Variable in class etomica.liquidLJ.MeterPU
temperature - Variable in class etomica.liquidLJ.MeterPUCut
temperature - Variable in class etomica.liquidLJ.MeterPUCutLS
temperature - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
temperature - Variable in class etomica.liquidLJ.MeterWidomInsertionP
temperature - Variable in class etomica.mappedvirial.MappedU.LJMDParams
temperature - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
temperature - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
temperature - Variable in class etomica.meam.EFSTungsten.Params
temperature - Variable in class etomica.metastable.LJmuVT.LJMCParams
temperature - Variable in class etomica.metastable.LJNPT.LJMCParams
temperature - Variable in class etomica.metastable.LJNVT.LJMCParams
temperature - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
temperature - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
temperature - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
temperature - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
temperature - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
temperature - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
temperature - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
temperature - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
temperature - Variable in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
temperature - Variable in class etomica.models.oneDHardRods.MeterCompareWVShortcut
temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
temperature - Variable in class etomica.models.oneDHardRods.MeterWidomMode
temperature - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
temperature - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
temperature - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
temperature - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
temperature - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
temperature - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
temperature - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
temperature - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
temperature - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
temperature - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
temperature - Variable in class etomica.modules.adsorption.EOSSW
temperature - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
temperature - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
temperature - Variable in class etomica.modules.render.RenderMD.RenderMDParam
temperature - Variable in class etomica.modules.vle.VLESim
temperature - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
temperature - Variable in class etomica.normalmode.IntegratorHarmonic
temperature - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
temperature - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
temperature - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
temperature - Variable in class etomica.normalmode.MCMoveHarmonic
temperature - Variable in class etomica.normalmode.MCMoveSingleMode
temperature - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
temperature - Variable in class etomica.normalmode.MCMoveVolumeSolid
temperature - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
temperature - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
temperature - Variable in class etomica.normalmode.MeterBoltzmannHTTP
temperature - Variable in class etomica.normalmode.MeterBoltzmannTarget
temperature - Variable in class etomica.normalmode.MeterDADB
temperature - Variable in class etomica.normalmode.MeterDDP
temperature - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
temperature - Variable in class etomica.normalmode.MeterDP
temperature - Variable in class etomica.normalmode.MeterOverlapSwitch
temperature - Variable in class etomica.normalmode.MeterSolidDA
temperature - Variable in class etomica.normalmode.MeterSolidDACut
temperature - Variable in class etomica.normalmode.MeterSolidMirror
temperature - Variable in class etomica.normalmode.MeterSolidProps
temperature - Variable in class etomica.normalmode.MeterSolidPropsLJ
temperature - Variable in class etomica.normalmode.MeterTargetTP
temperature - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
temperature - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
temperature - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
temperature - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
temperature - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
temperature - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
temperature - Variable in class etomica.normalmode.NormalModes1DHR
temperature - Variable in class etomica.normalmode.NormalModes2D
temperature - Variable in class etomica.normalmode.NormalModes3D
temperature - Variable in class etomica.normalmode.PotentialCalculationEFSSP
temperature - Variable in class etomica.normalmode.PotentialCalculationLJSP
temperature - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
temperature - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
temperature - Variable in class etomica.normalmode.SimBennet.SimBennetParam
temperature - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
temperature - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimLJVacancy.LJParams
temperature - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
temperature - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
temperature - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
temperature - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
temperature - Variable in class etomica.normalmode.WriteS
temperature - Variable in class etomica.overlap.MeterOverlap
temperature - Variable in class etomica.potential.EwaldSumMolecules
temperature - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
temperature - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
temperature - Variable in class etomica.potential.P2HePCKLJS.P2HeQFH
temperature - Variable in class etomica.potential.P2HePCKLJS.P2HeTI
temperature - Variable in class etomica.potential.P2HeSimplified.P2HeQFH
temperature - Variable in class etomica.potential.P2HeSimplified.P2HeTI
temperature - Variable in class etomica.potential.P2LJDipole
temperature - Variable in class etomica.potential.P2LJQ
temperature - Variable in class etomica.potential.P2LJQQ
temperature - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
temperature - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
temperature - Variable in class etomica.potential.P2SemiclassicalAtomic
temperature - Variable in class etomica.potential.P2SemiclassicalMolecular
temperature - Variable in class etomica.potential.PotentialCalculationPressureTensor
temperature - Variable in class etomica.surfacetension.LJMC.LJMCParams
temperature() - Method in class etomica.units.systems.CGS
temperature() - Method in class etomica.units.systems.LJ
temperature() - Method in class etomica.units.systems.MKS
temperature() - Method in class etomica.units.systems.UnitSystem.Sim
temperature() - Method in class etomica.units.systems.UnitSystem
Temperature - Class in etomica.units: The temperature dimension.
temperature - Variable in class etomica.virial.GUI.models.ModelTemperatureAndSteps
temperature - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
temperature - Variable in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
temperature - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
temperature - Variable in class etomica.virial.simulations.SimulationVirial
temperature - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
temperature - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
temperature - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
temperature - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
temperature - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
temperature - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
temperature - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
temperature - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
temperature - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
temperature - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
temperature - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
temperature - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
temperature - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
temperature - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
temperature - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
temperature - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
temperature - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
temperature - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
temperature - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
temperature - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
temperature - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
temperature - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
temperature - Variable in class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
temperature - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
temperature - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
temperature - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
temperature - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
temperature - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
temperature - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
temperature - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
temperature - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
temperature - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
temperature - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
temperature - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
temperature - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
temperature - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
temperature - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
temperature - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
temperature - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
temperature - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
temperature - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
temperature - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
temperature - Variable in class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
temperature - Static variable in class org.jmol.script.Token
temperature0 - Variable in class etomica.metastable.LJNVT.LJMCParams
temperatureAverage - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
temperatureDataSource - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
temperatureDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
temperatureHistory - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
temperatureK - Variable in class etomica.AlkaneEH.CH4NVT.Param
temperatureK - Variable in class etomica.dielectric.TIP4P_NVT.Param
temperatureK - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
temperatureK - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
temperatureK - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
temperatureK - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
temperatureK - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
temperatureK - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
temperaturePanel - Variable in class etomica.graphics.DeviceThermoSlider
temperatureSlider - Variable in class etomica.graphics.DeviceThermoSlider
temperatureVec - Variable in class etomica.integrator.IntegratorMD
tempImage - Variable in class etomica.space.BoundaryRectangularPeriodic
tempImage - Variable in class etomica.space.BoundaryRectangularPore
tempImage - Variable in class etomica.space.BoundaryRectangularSlit
template2 - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
template3 - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
templateName - Variable in class etomica.potential.PotentialEmul
tempOrientA - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
tempOrientA - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
tempOrientation - Variable in class etomica.integrator.IntegratorRigidIterative
tempOrientation - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
tempOrientB - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
tempOrientB - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
tempQuat - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
tempRotationTensor - Variable in class etomica.integrator.IntegratorRigidIterative
tempSet - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
tempSlider - Variable in class etomica.modules.adsorption.AdsorptionGraphic
tempSlider - Variable in class etomica.modules.catalysis.CatalysisGraphic
tempSlider - Variable in class etomica.modules.insertion.InsertionGraphic
tempSlider - Variable in class etomica.modules.mu.MuGraphic
tempSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
tempSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
tempSlider - Variable in class etomica.modules.swmd.SwmdGraphic
tempTens - Variable in class etomica.action.BoxInflateDeformable
tempTensInv - Variable in class etomica.action.BoxInflateDeformable
tempTensorkk - Variable in class etomica.potential.EwaldSummation
tempU - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
tempVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
tempVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
tensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
tensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
tensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
tensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
tensor - Variable in class etomica.models.nitrogen.TestRotationVector
Tensor - Interface in etomica.space
Tensor1D - Class in etomica.space1d: Implementation of a tensor for a 1-dimensional space.
Tensor1D() - Constructor for class etomica.space1d.Tensor1D: Default constructor sets tensor element to zero.
Tensor1D(double[][]) - Constructor for class etomica.space1d.Tensor1D
Tensor2D - Class in etomica.space2d: Implementation of a tensor for a 2-dimensional space.
Tensor2D() - Constructor for class etomica.space2d.Tensor2D: Default constructor sets all tensor elements to zero.
Tensor2D(double[][]) - Constructor for class etomica.space2d.Tensor2D: Constructs tensor with elements set by the given array.
Tensor3D - Class in etomica.space3d
Tensor3D() - Constructor for class etomica.space3d.Tensor3D: Default constructor sets all elements to zero.
Tensor3D(double[][]) - Constructor for class etomica.space3d.Tensor3D: Constructs tensor with elements set by the given array.
TensorND - Class in etomica.spaceNd
TensorND(int) - Constructor for class etomica.spaceNd.TensorND
tensorTrans - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
tensorWork - Variable in class etomica.models.nitrogen.P2Nitrogen
TERA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺¹².
ternaryAction(double, double, double) - Method in interface etomica.graphics.DeviceTernarySelector.Listener
test - Variable in class etomica.meam.PotentialCuLREP
TestAceticAcidMC3D_NPT - Class in etomica.association.AceticAcid: OPLS Acetic Acid Monte Carlo NPT simulation in 3D.
TestAceticAcidMC3D_NPT(int, double, double, double, long) - Constructor for class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
TestAceticAcidMC3D_NPT.AceticAcidMCParam - Class in etomica.association.AceticAcid
testBit(int) - Method in interface etomica.graph.model.Bitmap
testBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1).
testBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
TestDifferentImage1DHRAdd - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Output: histogram files of probability that a mode is zero Calculate free energy of solid Treats modes as degrees of freedom; uses a MeterDifferentImage to calculate what happens when an extra mode is added.
TestDifferentImage1DHRAdd(Space, int, double, int, int[]) - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
TestDifferentImage1DHRAdd.SimParam - Class in etomica.models.oneDHardRods
TestDifferentImage1DHRSubtract - Class in etomica.models.oneDHardRods: MC simulation 1D hard rods No graphic display Output: histogram files of probability that a mode is zero Calculate free energy of solid Treats modes as degrees of freedom; uses a MeterDifferentImage to calculate what happens when an extra mode is added.
TestDifferentImage1DHRSubtract(Space, int, double, int, int[]) - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
TestDifferentImage1DHRSubtract.SimParam - Class in etomica.models.oneDHardRods
Tester - Class in etomica.units
Tester() - Constructor for class etomica.units.Tester
TestEwaldTIP4PWater - Class in etomica.models.water
TestFiniteDifferenceDerivative - Class in etomica.conjugategradient
TestFiniteDifferenceDerivative() - Constructor for class etomica.conjugategradient.TestFiniteDifferenceDerivative
testflag1 - Static variable in class org.jmol.script.Token
testflag2 - Static variable in class org.jmol.script.Token
testflag3 - Static variable in class org.jmol.script.Token
testflag4 - Static variable in class org.jmol.script.Token
TestHC2YukawaMC3D - Class in etomica.yukawa: Hard-core plus two Yukawa fluid Monte-Carlo simulation in 3D
TestHC2YukawaMC3D() - Constructor for class etomica.yukawa.TestHC2YukawaMC3D
TestHC2YukawaMC3D(int) - Constructor for class etomica.yukawa.TestHC2YukawaMC3D
TestHexane - Class in etomica.models.hexane
TestHexane(Space, double, int, int, int) - Constructor for class etomica.models.hexane.TestHexane
TestHexaneCBMCOnly - Class in etomica.models.hexane
TestHexaneCBMCOnly(Space, int) - Constructor for class etomica.models.hexane.TestHexaneCBMCOnly
TestHexaneFileConfig - Class in etomica.models.hexane
TestHexaneFileConfig(Space, double, int, int, int) - Constructor for class etomica.models.hexane.TestHexaneFileConfig
TestHexaneHarmonic - Class in etomica.models.hexane
TestHexaneHarmonic(Space, int) - Constructor for class etomica.models.hexane.TestHexaneHarmonic
TestHexaneHarmonic.DataProcessorFoo - Class in etomica.models.hexane: DataProcessor that sums up the logs of all incoming values
TestHSMD3D - Class in etomica.tests: Simple hard-sphere molecular dynamics simulation in 3D.
TestHSMD3D(ISpace, int, int) - Constructor for class etomica.tests.TestHSMD3D
TestHSMD3D.SimParams - Class in etomica.tests
TestIGAssociationMC3D_NPT_DoubleSites - Class in etomica.association: Simple ideal gas + S-W Association Monte Carlo NPT simulation in 3D.
TestIGAssociationMC3D_NPT_DoubleSites(int, double, double, double, double, double, int, boolean, long) - Constructor for class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam - Class in etomica.association
TestLJAssociationMC3D_NPT - Class in etomica.association: Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NPT(int, double, double, double, double, long) - Constructor for class etomica.association.TestLJAssociationMC3D_NPT
TestLJAssociationMC3D_NPT - Class in etomica.virial.simulations: Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NPT(int, double, double, double, double, long) - Constructor for class etomica.virial.simulations.TestLJAssociationMC3D_NPT
TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam - Class in etomica.association
TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam - Class in etomica.virial.simulations
TestLJAssociationMC3D_NPT_DoubleSites - Class in etomica.association: Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NPT_DoubleSites(int, double, double, double, double, double, int, boolean, long) - Constructor for class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam - Class in etomica.association
TestLJAssociationMC3D_NVTOld - Class in etomica.association: Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
TestLJAssociationMC3D_NVTOld(int, double, double, double, double, long) - Constructor for class etomica.association.TestLJAssociationMC3D_NVTOld
TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam - Class in etomica.association
TestLJMC3D - Class in etomica.tests: Simple Lennard-Jones Monte Carlo simulation in 3D.
TestLJMC3D(int, int) - Constructor for class etomica.tests.TestLJMC3D
TestLJMC3D.SimParams - Class in etomica.tests
testMolecule - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
testMolecule - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
testMoleculeIndex - Variable in class etomica.modules.adsorption.MyMCMove
testMoleculeIndex - Variable in class etomica.modules.dcvgcmd.MyMCMove
TestNonLinearConjugateGradients - Class in etomica.conjugategradient
TestNonLinearConjugateGradients() - Constructor for class etomica.conjugategradient.TestNonLinearConjugateGradients
testOrthoCurvature(IVectorRandom[], IVectorRandom[]) - Method in class etomica.dimer.IntegratorDimerRT: Checks the curvature value at dimer orientation along a vector orthogonal to lowest curvature mode's (lcm) vector with the lcm's unit vector.
testPair(Graph, byte, byte, List) - Method in class etomica.graph.property.FFTDecomposition
testPair(Graph, byte, byte, List) - Method in class etomica.graph.property.IsFFT
TestRotationVector - Class in etomica.models.nitrogen
TestRotationVector() - Constructor for class etomica.models.nitrogen.TestRotationVector
TestSetToUHexane - Class in etomica.models.hexane
TestSWChain - Class in etomica.tests: Simple square-well chain simulation.
TestSWChain(ISpace, int, double) - Constructor for class etomica.tests.TestSWChain
TestSWChain.SimParams - Class in etomica.tests
testTransformVector(IVector) - Method in class etomica.space.BoundaryDeformablePeriodic: We test the given vector (v) to see if 0.5*v would be transformed by any of our existing transformVectors.
TestYukawaMC3D - Class in etomica.yukawa: A Yukawa Monte-Carlo simulation in 3D
TestYukawaMC3D() - Constructor for class etomica.yukawa.TestYukawaMC3D
TestYukawaMC3D(int) - Constructor for class etomica.yukawa.TestYukawaMC3D
TestYukawaMD3D - Class in etomica.yukawa: A Yukawa MD Simulation adapted from HSMD3D simulation prototype.
TestYukawaMD3D() - Constructor for class etomica.yukawa.TestYukawaMD3D
tetherBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
tetherBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
tetraNum - Variable in class etomica.data.meter.MeterDihedralAngle
textAreaForBonds - Variable in class etomica.modules.clustergenerator.MyApplet
textField - Variable in class etomica.graphics.DeviceBox: Object for displaying the value as a text field
textField - Variable in class etomica.graphics.DeviceSlider: To show the values of slider
TextFormat - Class in org.jmol.util
TextFormat() - Constructor for class org.jmol.util.TextFormat
thermalButtons - Variable in class etomica.graphics.DeviceThermoSlider
thermometer - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
thermometer - Variable in class etomica.modules.dcvgcmd.DCVGCMD
thermometer - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
thermometer - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
thermostat - Variable in class etomica.integrator.IntegratorMD
thermostatActions - Variable in class etomica.normalmode.IntegratorHardMDMC
thermostatCount - Variable in class etomica.integrator.IntegratorMD
thermostatInterval - Variable in class etomica.integrator.IntegratorMD
thermostatNoDrift - Variable in class etomica.integrator.IntegratorMD
thermostatting - Variable in class etomica.integrator.IntegratorMD
ThermostatType(String) - Constructor for class etomica.integrator.IntegratorMD.ThermostatType
thermostatType - Variable in class etomica.modules.render.RenderMD.RenderMDParam
THETA - Variable in class etomica.dimer.IntegratorDimerMin
THETA - Variable in class etomica.dimer.IntegratorDimerRT
theta - Variable in class etomica.normalmode.HSDimerNPT
theta - Variable in class etomica.potential.P2QChemInterpolated
theta - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
theta - Static variable in class org.jmol.script.Token
thetaFrac - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
thetaFrac - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
thetaSlider - Variable in class etomica.modules.sam.SamGraphic
THETAstar - Variable in class etomica.dimer.IntegratorDimerMin
THETAstar - Variable in class etomica.dimer.IntegratorDimerRT
THETAstarstar - Variable in class etomica.dimer.IntegratorDimerRT
thirdAxis - Variable in class etomica.association.BiasVolume2SiteAceticAcid
thirdAxis - Variable in class etomica.association.BiasVolumeAceticAcid
thisBox(IBox) - Static method in class etomica.util.Debug: Checks whether the given box is of debugging interest
threadCalculate - Variable in class etomica.threaded.atom.PotentialMasterListWorker
threadCalculate - Variable in class etomica.threaded.domain.PotentialMasterListWorker
threadList - Variable in class etomica.threaded.atom.PotentialMasterListWorker
threadList - Variable in class etomica.threaded.domain.PotentialMasterListWorker
threadNumber - Variable in class etomica.threaded.atom.PotentialMasterListWorker
threadNumber - Variable in class etomica.threaded.domain.PotentialMasterListWorker
ThreadsMD - Class in etomica.threads
ThreadsMD(int, int, int, int, double, double[][], double[][], double[][], AtomDecompositionMD) - Constructor for class etomica.threads.ThreadsMD
threej(int, int, int, int, int, int) - Static method in class etomica.potential.P2O2Bartolomei
threesqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
threesqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
threshold - Variable in class etomica.graphics.DeviceDelaySlider
ti - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
TIFF - Static variable in class etomica.graph.view.rasterizer.DestinationType
TIFF_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
TIFF_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
TIFF_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
Tij - Variable in class etomica.models.co2.PNCO2GCPM
Tij - Variable in class etomica.models.water.PNWaterGCPM
tilt - Variable in class etomica.util.numerical.AkimaSplineSmootherApp.PlotAction
tilt - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp.PlotAction
time - Variable in class etomica.graph.traversal.Biconnected
time - Variable in class etomica.integrator.IntegratorAnalytic.AtomTimeAction
time() - Method in class etomica.units.systems.CGS
time() - Method in class etomica.units.systems.LJ
time() - Method in class etomica.units.systems.MKS
time() - Method in class etomica.units.systems.UnitSystem.Sim
time() - Method in class etomica.units.systems.UnitSystem
Time - Class in etomica.units: Dimension for all units of time.
TIMEDBALL - Static variable in class g3dsys.control.G3DSys
TimeOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.TimeOptionHandler
timer - Variable in class etomica.graphics.DisplayTimer
times(Complex) - Method in class etomica.math.Complex: Complex multiplication (doesn't change this Complex number).
times(Matrix) - Method in class etomica.math.linearalgebra.Matrix
times(Rational) - Method in class etomica.util.Rational: Returns a new Rational instance, which is the result of multiplying this Rational by the given Rational.
timeStep - Variable in class etomica.integrator.IntegratorMD
timeStep - Variable in class etomica.modules.render.RenderMD.RenderMDParam
timlim - Static variable in class etomica.potential.P2WaterPotentialsJankowski
Tin - Class in etomica.chem.elements: Class for the Tin element.
Tin(String) - Constructor for class etomica.chem.elements.Tin
Tin(String, double) - Constructor for class etomica.chem.elements.Tin
TIP4P_NVT - Class in etomica.dielectric: Canonical ensemble Monte Carlo simulation (NVT) dielectric constant (epsilon) TIP4P water
TIP4P_NVT(Space, int, double, double, double, double) - Constructor for class etomica.dielectric.TIP4P_NVT
TIP4P_NVT.DipoleSourceTIP4PWater - Class in etomica.dielectric
TIP4P_NVT.Param - Class in etomica.dielectric
tKelvin - Variable in class etomica.potential.P2WaterPotentialsJankowski
tmp - Variable in class etomica.overlap.DataOverlap
tmpAtomicTensor3 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
tmpDrr - Variable in class etomica.models.water.P2Water4PSoft
tmpDrr1 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
tmpSecondD - Variable in class etomica.models.water.P2Water4PSoft
tmpTensor - Variable in class etomica.models.water.P2Water4PSoft
toArray() - Method in class etomica.atom.AtomArrayList
toArray() - Method in class etomica.atom.MoleculeArrayList
toArray() - Method in class etomica.graph.model.GraphList
toArray(T[]) - Method in class etomica.graph.model.GraphList
toArray() - Method in interface etomica.space.Tensor
toArray() - Method in class etomica.space1d.Tensor1D
toArray() - Method in class etomica.space2d.Tensor2D: Returns tensor in an array, writing rowwise, i.e., in order xx, xy, yx, yy.
toArray() - Method in class etomica.space3d.Tensor3D: Returns tensor in a new array, writing elements row-wise, i.e.: xx, xy, xz, yx, yy, yz, zx, zy, zz;
toArray() - Method in class etomica.spaceNd.TensorND
toArray() - Method in class etomica.util.ObjectArrayList: Returns an array containing all of the elements in this list in the correct order.
toArray(Object[]) - Method in class etomica.util.ObjectArrayList: Returns an array containing all of the elements in this list in the correct order.
toArray() - Method in class org.jmol.script.ScriptVariable
toAtomLeafArray() - Method in class etomica.atom.AtomArrayList
toAxisAngle4f() - Method in class org.jmol.util.Quaternion
toBytes(int, int) - Method in class org.jmol.util.StringXBuilder: simple byte conversion not allowing for unicode.
toCanonical - Static variable in class org.jmol.util.BoxInfo
toE(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations: Returns an array of cluster diagrams with all e-bonds representing the same sum of diagrams as the given f-bond cluster.
toE(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations: Returns an array of cluster diagrams with all e-bonds representing the same sum of diagrams as the given f-bond clusters.
toFString(int) - Method in class etomica.veos.bigdecimal.Rational: Return a string in floating point format.
toggle() - Method in class etomica.graphics.DeviceCheckBox: Toggles the state of the button (true to false, false to true).
toggleAction - Variable in class etomica.graphics.DeviceToggleButton
toggleInPlace(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil: a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.
toIfactor(int) - Method in class etomica.veos.bigdecimal.Factorial: Compute the factorial of the non-negative integer.
toInt() - Method in class etomica.graph.view.rasterizer.DestinationType
toJSON(String, Object) - Static method in class org.jmol.util.Escape
tok - Variable in class org.jmol.script.Token
tokAttr(int, int) - Static method in class org.jmol.script.Token
tokAttrOr(int, int, int) - Static method in class org.jmol.script.Token
Token - Class in org.jmol.script
Token() - Constructor for class org.jmol.script.Token
Token(int) - Constructor for class org.jmol.script.Token
tokenAnd - Static variable in class org.jmol.script.Token
tokenAND - Static variable in class org.jmol.script.Token
tokenAndFALSE - Static variable in class org.jmol.script.Token
tokenComma - Static variable in class org.jmol.script.Token
tokenConnected - Static variable in class org.jmol.script.Token
tokenExpressionBegin - Static variable in class org.jmol.script.Token
tokenExpressionEnd - Static variable in class org.jmol.script.Token
tokenLeftParen - Static variable in class org.jmol.script.Token
tokenOpIf - Static variable in class org.jmol.script.Token
tokenOr - Static variable in class org.jmol.script.Token
tokenOrTRUE - Static variable in class org.jmol.script.Token
tokenRightParen - Static variable in class org.jmol.script.Token
tol - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
tol - Variable in class etomica.virial.ClusterWheatleySoft
tol - Variable in class etomica.virial.ClusterWheatleySoftBD
tolerance - Variable in class etomica.models.nitrogen.FindTransitionTemperature
tolerance - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
tolerance - Variable in class etomica.modules.interfacial.FitTanh
tolerance - Variable in class etomica.normalmode.SoftSphereSolidEOS
tolerance - Variable in class etomica.surfacetension.FitTanh
tolerance - Variable in class etomica.util.HistogramDiscrete
tolf - Static variable in class etomica.potential.P2WaterPotentialsJankowski
toList(Object[]) - Static method in class etomica.util.Arrays: Creates a new LinkedList filled with the elements of the given array, in the same order.
tolr - Static variable in class etomica.potential.P2WaterPotentialsJankowski
toMoleculeArray() - Method in class etomica.atom.MoleculeArrayList
toNumberString() - Method in interface etomica.graph.model.Bitmap: Returns a string for the integer represented by this bitmap
toNumberString() - Method in class etomica.graph.model.impl.AbstractBitmap
toolbar - Variable in class etomica.graphics.SimulationPanel
toolbarPanel - Variable in class etomica.graphics.SimulationPanel
TOP - Static variable in class etomica.graphics.DisplayBox
TOP - Static variable in class etomica.graphics.DisplayPolytope
TOP - Static variable in class etomica.math.Gamma
TOP - Static variable in class etomica.util.Constants.Direction
toPattern() - Method in class etomica.util.ScientificFormat
TOPEXP - Static variable in class etomica.math.Gamma
toPixels() - Method in class etomica.units.Pixel
toPoint4f() - Method in class org.jmol.util.Quaternion
topPadding - Variable in class etomica.interfacial.ConfigurationLammps
toPString() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Print as a polyomial in x.
topWall - Variable in class etomica.interfacial.MeterWallForce
toRational() - Method in class etomica.veos.bigdecimal.BigSurd: Convert to a rational value if possible
toRatPoly() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Translate into a RatPoly copy.
toReadable(String, Object) - Static method in class org.jmol.util.Escape
torque() - Method in interface etomica.integrator.Integrator.Torquable
torque - Variable in class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
torque() - Method in class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
torque - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
torque() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
torque - Variable in class etomica.models.co2.P2CO2H2OWheatley
torque - Variable in class etomica.models.co2.P2CO2Hellmann
torque - Variable in class etomica.models.nitrogen.P2Nitrogen
torque - Variable in class etomica.models.water.P2Water3PSoft
torque - Variable in class etomica.models.water.P2Water4PSoft
torque - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
torque - Variable in class etomica.potential.P2HSDipole
torque - Variable in class etomica.potential.P2LJDipole
torque - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
torque - Variable in class etomica.rotation.P2LJDipole
torqueF - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
torqueSum - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
torqueSum - Variable in class etomica.integrator.IntegratorRigidIterative
torqueSum - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
torqueSum - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
torqueSum - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
torsionPotential - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
torsionPotential - Variable in class etomica.virial.MCMoveClusterTorsionMulti
toSim(double) - Method in class etomica.units.CompoundUnit
toSim(double) - Method in class etomica.units.PrefixedUnit: Takes the given value in class units (considering prefix) and converts it to simulation units.
toSim(double) - Method in class etomica.units.SimpleUnit: Takes the given value in class units and converts it to simulation units.
toSim(double) - Method in class etomica.units.systems.LJ.LJUnit
toSim(double) - Method in interface etomica.units.Unit: Takes the given value in class units (considering prefix) and converts it to simulation units.
toSpherical(IVector, double[]) - Static method in class etomica.math.geometry.coordinate.CoordinateConverter
toString() - Method in class etomica.action.activity.Controller
toString() - Method in class etomica.atom.Atom: Returns a string formed by concatenating the signature of this atom to a string that identifies it as a species master, species agent, molecule, group, or (leaf) atom.
toString() - Method in class etomica.atom.AtomArrayList
toString() - Method in class etomica.atom.AtomPair
toString() - Method in class etomica.atom.AtomsetArray
toString() - Method in class etomica.atom.AtomSetSinglet
toString() - Method in class etomica.atom.Molecule: Returns a string formed by concatenating the signature of this atom to a string that identifies it as a molecule.
toString() - Method in class etomica.atom.MoleculePair
toString() - Method in class etomica.atom.MoleculesetArray
toString() - Method in class etomica.atom.MoleculeSetSinglet
toString() - Method in class etomica.box.Box
toString() - Method in class etomica.data.DataAccumulator: Overrides the Object class toString method to have it return the output of dataInfo.getLabel()
toString() - Method in class etomica.data.DataInfo: Returns "label (dimension)", where label and dimension are the values held by this instance.
toString() - Method in interface etomica.data.IDataInfo: Returns "label (dimension)", where label and dimension are the values held by this instance.
toString() - Method in class etomica.data.types.DataDouble: Returns a string formed from the dataInfo label and this value.
toString() - Method in class etomica.data.types.DataDoubleArray: Returns a string formed from the dataInfo label and the array values.
toString() - Method in class etomica.data.types.DataDoubleBDArray: Returns a string formed from the dataInfo label and the array values.
toString() - Method in class etomica.data.types.DataGroup: Returns a string formed from the encapsulated data objects.
toString() - Method in class etomica.data.types.DataTensor: Returns a string formed from the dataInfo label and the tensor values.
toString() - Method in class etomica.data.types.DataVector: Returns a string formed from the dataInfo label and the vector values.
toString() - Method in class etomica.graph.isomorphism.NodePair
toString() - Method in class etomica.graph.model.GraphList
toString() - Method in class etomica.graph.model.impl.AbstractBitmap
toString() - Method in class etomica.graph.model.impl.CoefficientImpl
toString() - Method in class etomica.graph.model.impl.EdgeImpl
toString() - Method in class etomica.graph.model.impl.GraphImpl
toString() - Method in class etomica.graph.model.impl.MetadataImpl
toString() - Method in class etomica.graph.model.impl.NodeImpl
toString() - Method in class etomica.graph.view.rasterizer.DestinationType
toString(String[]) - Method in class etomica.graph.view.rasterizer.Main
toString() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
toString() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
toString() - Method in class etomica.graphics.Display: Overrides the Object class toString method to have it return the output of getName
toString() - Method in class etomica.integrator.IntegratorHard.Agent
toString() - Method in class etomica.integrator.mcmove.MCMove
toString() - Method in class etomica.integrator.mcmove.MCMoveBox
toString() - Method in class etomica.lattice.crystal.PrimitiveBcc
toString() - Method in class etomica.lattice.crystal.PrimitiveCubic
toString() - Method in class etomica.lattice.crystal.PrimitiveFcc
toString() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
toString() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
toString() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
toString() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
toString() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
toString() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
toString() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
toString() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
toString() - Method in class etomica.lattice.LatticeCubicBcc: Returns "Bcc".
toString() - Method in class etomica.lattice.LatticeCubicDiamond: Returns "Diamond".
toString() - Method in class etomica.lattice.LatticeCubicFcc: Returns "Fcc".
toString() - Method in class etomica.lattice.LatticeCubicSimple: Returns "Simple cubic".
toString() - Method in class etomica.lattice.LatticeHcp
toString() - Method in class etomica.lattice.LatticeOrthorhombicHexagonal: Returns "OrthorhombicHexagonal".
toString() - Method in class etomica.math.Complex: String representation of this Complex number.
toString() - Method in class etomica.math.geometry.Point
toString() - Method in class etomica.math.geometry.Polytope
toString() - Method in class etomica.math.Quaternion: Returns the string representation of the Quaternion q
toString() - Method in class etomica.models.hexane.PrimitiveHexane
toString() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
toString() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
toString() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
toString() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
toString() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
toString() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
toString() - Method in class etomica.space1d.Vector1D
toString() - Method in class etomica.space2d.Tensor2D
toString() - Method in class etomica.space2d.Vector2D
toString() - Method in class etomica.space3d.Tensor3D
toString() - Method in class etomica.space3d.Vector3D
toString() - Method in class etomica.spaceNd.TensorND
toString() - Method in class etomica.spaceNd.VectorND
toString() - Method in class etomica.units.Dimension
toString() - Method in class etomica.units.Prefix
toString() - Method in class etomica.units.PrefixedUnit: Accessor for common name of baseUnit
toString() - Method in class etomica.units.SimpleUnit: Accessor for common name of unit
toString(int[]) - Static method in class etomica.util.Arrays: Converts the given array of integers into a string with a comma-separated list of the integers enclosed by braces.
toString(double[]) - Static method in class etomica.util.Arrays: Converts the given array of doubles into a string with a comma-separated list of the doubles enclosed by braces.
toString(float[]) - Static method in class etomica.util.Arrays: Converts the given array of floats into a string with a comma-separated list of the floats enclosed by braces.
toString(boolean[]) - Static method in class etomica.util.Arrays: Converts the given array of booleans into a string with a comma-separated list of the booleans enclosed by braces.
toString() - Method in class etomica.util.DoubleRange: Returns String of the form [min,max]
toString() - Method in class etomica.util.EnumeratedType
toString() - Method in class etomica.util.IntegerRange: Returns String of the form [min,max]
toString() - Method in class etomica.util.Rational
toString() - Method in class etomica.util.TreeLinker
toString() - Method in class etomica.veos.bigdecimal.BigComplex: Human-readable Fortran-type display
toString(MathContext) - Method in class etomica.veos.bigdecimal.BigComplex: Human-readable Fortran-type display
toString() - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Print as a comma-separated list of coefficients.
toString() - Method in class etomica.veos.bigdecimal.BigSurd: Return a string in the format (number/denom)*()^(1/2).
toString() - Method in class etomica.veos.bigdecimal.BigSurdVec: Return a string in the format (number/denom)*()^(1/2).
toString() - Method in class etomica.veos.bigdecimal.Ifactor: Convert to printable format
toString() - Method in class etomica.veos.bigdecimal.Rational: Return a string in the format number/denom.
toString() - Method in class etomica.virial.cluster.ClusterDiagram
toString() - Method in class etomica.virial.ClusterBonds
toString() - Method in class etomica.virial.IntSet
toString() - Method in class etomica.virial.MCMoveClusterAtomQ
toString() - Method in class org.jmol.script.ScriptVariable
toString() - Method in class org.jmol.script.Token
toString() - Method in class org.jmol.util.AxisAngle4f: Returns a string that contains the values of this AxisAngle4f.
toString() - Method in class org.jmol.util.BitSet: Returns a string representation of this bit set.
toString() - Method in class org.jmol.util.Matrix3f: Returns a string that contains the values of this Matrix3f.
toString() - Method in class org.jmol.util.Matrix4f: Returns a string that contains the values of this Matrix4f.
toString() - Method in class org.jmol.util.Quadric
toString() - Method in class org.jmol.util.Quaternion: Java axisAngle / plane / Point4f format all have the format {x y z w} so we go with that here as well
toString() - Method in class org.jmol.util.Rgb16
toString() - Method in class org.jmol.util.StringXBuilder
toString() - Method in class org.jmol.util.Tuple3f: Returns a string that contains the values of this Tuple3f.
toString() - Method in class org.jmol.util.Tuple3i: Returns a string that contains the values of this Tuple3i.
toString() - Method in class org.jmol.util.Tuple4f: Returns a string that contains the values of this Tuple4f.
toStringArray(Object[]) - Static method in class etomica.util.Strings: Takes an array of objects and converts them to an array of strings, with each string given by the object's toString method.
toSVG(int) - Method in interface etomica.graph.model.Graph
toSVG(int) - Method in class etomica.graph.model.impl.GraphImpl
tot - Variable in class etomica.virial.ClusterICPYC
total - Static variable in class etomica.graph.isomorphism.Match
total - Static variable in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
total - Variable in class etomica.modules.chainequilibrium.MeterConversion
total - Variable in class etomica.virial.ClusterWheatleyHS
total - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
total - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
totalAtomCount - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
totalAtoms - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
totalAtoms - Variable in class etomica.virial.SpeciesAlkaneEH
totalBlockSum - Variable in class etomica.data.AccumulatorAverageCollapsing
totalCells - Variable in class etomica.threaded.domain.NeighborCellManagerThreaded
totalChildCount - Variable in class etomica.species.SpeciesSpheresHetero
totalCount - Variable in class etomica.util.HistogramDiscrete
totalCount - Variable in class etomica.virial.MCMoveClusterAtomHSRing
totalCount - Variable in class etomica.virial.MeterVirialBDBin
totalCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
totalCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded
totalCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
totalCount - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
totalCount - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
totalDeleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
totalDeleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
totalMass - Variable in class etomica.models.water.PNWaterGCPM
totalMolecules - Variable in class etomica.virial.MayerFunctionThreeBody
totalNCluster - Variable in class etomica.modules.clustergenerator.MyApplet
totalSteps - Variable in class etomica.data.DataPumpListenerPow
totalSum - Variable in class etomica.util.HistogramNotSoSimple
totalSumBlockSq - Variable in class etomica.data.AccumulatorAverageCollapsing
totalSumSquare - Variable in class etomica.data.AccumulatorAverageCollapsing
totNumSubSteps - Variable in class etomica.overlap.IntegratorOverlap
totPCore - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
totSqErr - Variable in class etomica.util.numerical.AkimaSplineSmoother
totTime - Variable in class etomica.overlap.IntegratorOverlap
toWriteFile - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
Tprod(IVector, IVector, IVector, double) - Method in class etomica.models.water.P2WaterSzalewicz: Calculate the vector V resulting from the action of the dipole propagator tensor T_ij on U Ri, Rj - position vectors of molecules i and j, respectively rij = |Ri - Rj|^(-3)
tqli(double[], double[], int) - Method in class etomica.math.linearalgebra.EigenSystemTriDiagonal
trace() - Method in interface etomica.space.Tensor
trace() - Method in class etomica.space1d.Tensor1D
trace() - Method in class etomica.space2d.Tensor2D
trace() - Method in class etomica.space3d.Tensor3D
trace() - Method in class etomica.spaceNd.TensorND
trace - Static variable in class org.jmol.script.Token
tracealpha - Static variable in class org.jmol.script.Token
tracker - Variable in class etomica.config.ConformationChain2D
trajectory - Static variable in class org.jmol.script.Token
transcode(SVGConverterSource, File, Transcoder) - Method in class etomica.graph.view.rasterizer.SVGConverter: Converts the input image to the result image.
transform(IVectorMutable) - Method in interface etomica.space.Tensor: Applies the given tensor transformation to this vector, replaced its elements with the transformed values.
transform(IVectorMutable) - Method in class etomica.space1d.Tensor1D
transform(IVectorMutable) - Method in class etomica.space2d.Tensor2D
transform(IVectorMutable) - Method in class etomica.space3d.Tensor3D
transform(IVectorMutable) - Method in class etomica.spaceNd.TensorND
transform() - Method in class etomica.util.FastFourierTransform: Forward Transformation of discrete data sets
Transform - Interface in etomica.util: Function interface that takes an array of doubles and returns a transformed array of doubles
transform(IMolecule, double) - Method in class etomica.virial.MCMoveClusterAngleBend
transform(IMolecule, double) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
transform(Tuple3f) - Method in class org.jmol.util.Matrix3f
transform(Point3f) - Method in class org.jmol.util.Matrix4f: Transforms the point parameter with this Matrix4f and places the result back into point.
transform(Vector3f) - Method in class org.jmol.util.Quaternion
Transform.Fourier - Class in etomica.util
transform2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Matrix3f: Transform the vector vec using this Matrix3f and place the result into vecOut.
transform2(Point3f, Point3f) - Method in class org.jmol.util.Matrix4f: Transforms the point parameter with this Matrix4f and places the result into pointOut.
transform4(Tuple4f) - Method in class org.jmol.util.Matrix4f: Transform the vector vec using this Matrix4f and place the result back into vec.
TransformManager - Class in g3dsys.control
transformP2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Quaternion
transformPoints(List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
transformPt(Point3f) - Method in class org.jmol.util.Quaternion
transformT2(Tuple4f, Tuple4f) - Method in class org.jmol.util.Matrix4f: Transform the vector vec using this Matrix4f and place the result into vecOut.
transformV(Vector3f) - Method in class org.jmol.util.Matrix4f: Transforms the normal parameter by this transform and places the value back into normal.
transformV2(Vector3f, Vector3f) - Method in class org.jmol.util.Matrix4f: Transforms the normal parameter by this Matrix4f and places the value into normalOut.
transformVectors - Variable in class etomica.space.BoundaryDeformablePeriodic
translate - Static variable in class org.jmol.script.Token
translateBy - Variable in class etomica.integrator.IntegratorRigidIterative
translateBy - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
translateBy - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
translateBy - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
translateBy - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
translateBy - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
translateBy - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
translateBy - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
translateBy - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
translateBy - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
translateBy - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
translateBy - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
translateBy - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
translateBy - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
translateBy - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
translateBy - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
translateDimerQuickmin() - Method in class etomica.dimer.IntegratorDimerRT: Moves the dimer along the lowest curvature mode of the energy surface, Quickmin style.
translateMonomerB() - Method in class etomica.action.IntegratorDimerApproach
translateTo - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
translateTo - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
translation(double[], double[], IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
translation(double[], double[], double[], IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
translation - Static variable in class org.jmol.script.Token
translation2Mol(int, double[], IBox) - Method in class etomica.virial.ConfigurationClusterAceticAcid
translation3Mol(double[], double[], IBox) - Method in class etomica.virial.ConfigurationClusterAceticAcid
translationRandom(IMolecule, IBox) - Method in class etomica.virial.ConfigurationClusterAceticAcid
translationTetramer(double[], double[], double[], IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
translationTrimer(double[], double[], IBox) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
translationVector - Variable in class etomica.action.BoxInflateAnisotropic
translationVector - Variable in class etomica.action.IntegratorDimerApproach
translationVector() - Method in class etomica.action.IntegratorDimerApproach
translationVector - Variable in class etomica.association.MCMoveDimer
translationVector - Variable in class etomica.association.MCMoveSmer
translationVector - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
translationVector - Variable in class etomica.integrator.mcmove.MCMoveAtom
translationVector - Variable in class etomica.integrator.mcmove.MCMoveDimer
translationVector - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
translationVector - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
translationVector - Variable in class etomica.normalmode.MCMoveAtomCoupled
translationVector - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
translationVector - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
translationVector - Variable in class etomica.normalmode.MCMoveAtomSuperBox
translationVectors - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
translationVectors - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
translationVectors - Variable in class etomica.virial.MCMoveClusterAtomMulti
translationVectors - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
translationVectors - Variable in class etomica.virial.MCMoveClusterRotateCH3
translationVectors - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
translationVectors - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
translationVectors - Variable in class etomica.virial.MCMoveClusterWiggleMulti
translator - Variable in class etomica.action.BoxInflate
translator - Variable in class etomica.integrator.IntegratorRigidIterative
translator - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
translator - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
translator - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
translator - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
translator - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
translucencyMask - Variable in class org.jmol.g3d.Graphics3D
translucent - Static variable in class org.jmol.script.Token
TRANSLUCENT_50 - Static variable in class org.jmol.util.Colix
TRANSLUCENT_MASK - Static variable in class org.jmol.util.Colix
TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.Colix
TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.Colix
translucentCoverOnly - Variable in class org.jmol.g3d.Graphics3D
TRANSPARENT - Static variable in class org.jmol.util.Colix
transpose() - Method in class etomica.math.linearalgebra.Matrix
transpose() - Method in interface etomica.space.Tensor
transpose() - Method in class etomica.space1d.Tensor1D
transpose() - Method in class etomica.space2d.Tensor2D
transpose() - Method in class etomica.space3d.Tensor3D
transpose() - Method in class etomica.spaceNd.TensorND
transpose() - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to its transpose.
transpose() - Method in class org.jmol.util.Matrix4f: Sets the value of this matrix to its transpose.
transposed - Variable in class etomica.graphics.DisplayTable
transposeM(Matrix3f) - Method in class org.jmol.util.Matrix3f: Sets the value of this matrix to the transpose of the argument matrix
transVect - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
tRatio - Variable in class etomica.virial.MeterVirialBDBin
tRatio - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
tRatio - Static variable in class etomica.virial.MeterVirialBinMultiThreaded
tRatio - Static variable in class etomica.virial.MeterVirialEBinMultiThreaded
tRatio - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
tRatio - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
tRatio - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
tRatio - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
Traversal - Interface in etomica.graph.traversal: This interface generalizes algorithms that traverse the nodes of a graph.
TraversalVisitor - Interface in etomica.graph.traversal
traverseAll(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal: The only reason to override this method is to change the node choice before traversing each component, or to traverse more complex components such as biconnected, K-connected, etc.
traverseAll(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.BiconectedNodalPoint: A variation of BCTraversal that only traverses connected components starting with field nodes.
traverseAll(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.Biconnected
traverseAll(Graph, TraversalVisitor) - Method in interface etomica.graph.traversal.Traversal: Traverses all components of the graph, starting at an arbitrary node for each component, and returns the total number of components traversed.
traverseBCC(byte, Graph, boolean) - Method in class etomica.graph.traversal.Biconnected
traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.AbstractTraversal
traverseComponent(byte, Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal: There should be no reason to override this method.
traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.Biconnected
traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.BreadthFirst
traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.DepthFirst
traverseComponent(byte, Graph, TraversalVisitor) - Method in interface etomica.graph.traversal.Traversal: Traverses a single component of the graph starting at the designated node.
tred2(double[][], int) - Method in class etomica.math.linearalgebra.EigenSystemReduction
TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
TREE - Static variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
TREE_CHAIN - Static variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
TREE_CHAIN_RING - Static variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
treeFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
TreeLinker - Class in etomica.util: Linker used in the binary tree TreeList.
TreeLinker(Object) - Constructor for class etomica.util.TreeLinker: Constructor throws exception if given atom is null.
TreeList - Class in etomica.util: TreeList is a generic binary tree structure made up of TreeLinkers.
TreeList() - Constructor for class etomica.util.TreeList
trialCount - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
trialNotify() - Method in class etomica.virial.BoxCluster: Inform the box that a trial move has been made so it can update the coordinate pairs.
trialP - Variable in class etomica.util.numerical.AkimaSplineSmoother
Triangle - Class in g3dsys.images: Class for drawing triangles (possibly making up a polygon)
Triangle(G3DSys, short, Point3f, Point3f, Point3f) - Constructor for class g3dsys.images.Triangle
TriangleData - Class in org.jmol.util
TriangleData() - Constructor for class org.jmol.util.TriangleData
triangles - Static variable in class org.jmol.script.Token
triangleTable2 - Static variable in class org.jmol.util.TriangleData
trim - Static variable in class org.jmol.script.Token
trim(String, String) - Static method in class org.jmol.util.TextFormat
trimerPotential - Variable in class etomica.association.MCMoveSmer
trimerPotential - Variable in class etomica.association.MCMoveSmerRotate
trimThreshold - Variable in class etomica.atom.AtomArrayList
trimThreshold - Variable in class etomica.atom.MoleculeArrayList
trimToSize() - Method in class etomica.atom.AtomArrayList
trimToSize() - Method in class etomica.atom.MoleculeArrayList
trimToSize() - Method in class etomica.util.ObjectArrayList: Trims the capacity of this ArrayList instance to be the list's current size.
tripletDone - Variable in class etomica.virial.PotentialCommonAtomic
tripletDone - Variable in class etomica.virial.PotentialGroup3PI
tripletId(int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams: Returns the triplet ID for the given indices (id0, id1, id2) and given number of molecules (n).
tripletId(int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT: Returns the triplet ID for the given indices (id0, id1, id2) and given number of molecules (n).
TripletInnerSequential - Class in etomica.atom.iterator
TripletInnerSequential() - Constructor for class etomica.atom.iterator.TripletInnerSequential
tripletStart - Static variable in class etomica.virial.cluster.VirialDiagrams
tripletStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
trueButton() - Method in class etomica.graphics.DeviceToggleRadioButtons
trueDataSink - Variable in class etomica.data.DataProcessor
trueDataSource - Variable in class etomica.modules.multiharmonic.DataProcessorBias
trueMultiP - Variable in class etomica.virial.cluster.VirialDiagrams
trueMultiP - Variable in class etomica.virial.cluster.VirialDiagramsPT
trueY - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
trunc(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Truncate polynomial degree.
trunc() - Method in class etomica.veos.bigdecimal.Rational: Remove the fractional part.
TruncatedOctahedron - Class in etomica.math.geometry: A truncated octahedron is an Archimedean, space-filling polyhedron with 24 vertices, 36 edges, and 14 faces.
TruncatedOctahedron(ISpace) - Constructor for class etomica.math.geometry.TruncatedOctahedron: Constructs a truncated octahedron with vertices defined in the embedded space and with unit edge lengths.
TruncatedOctahedron(ISpace, double) - Constructor for class etomica.math.geometry.TruncatedOctahedron: Constructs a truncated octahedron with vertices defined in the embedded space and with edge lengths equal to the given value.
truncatedPotential - Variable in class etomica.potential.Potential0Lrc
truncation - Variable in class etomica.AlkaneEH.CH4NVT.Param
truncation - Variable in class etomica.parser.ParserLAMMPS.Options
truncation - Variable in class etomica.potential.PotentialGroupSoft
truncationRadius - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
truncationRadius - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
truncationRadius - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
truncationRadius - Variable in class etomica.space.BoundaryDeformablePeriodic
trycmd - Static variable in class org.jmol.script.Token
TSelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
tStep - Variable in class etomica.interfacial.LJMD.LJMDParams
tStep - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
tStep - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
tStepFac - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
tt0Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
tt0Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
tt0Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
tt0Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
tt1Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
tt1Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
tt1Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
tTmp - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
tttprod - Static variable in class etomica.potential.P2WaterPotentialsJankowski
TTTprod(IVectorMutable, IVectorMutable, IVectorMutable, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
tunable - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
Tungsten - Class in etomica.chem.elements: Class for the Tungsten element.
Tungsten(String) - Constructor for class etomica.chem.elements.Tungsten
Tungsten(String, double) - Constructor for class etomica.chem.elements.Tungsten
Tunit - Variable in class etomica.models.co2.PNCO2GCPM
Tunit - Variable in class etomica.models.water.PNWaterGCPM
tUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
tUnit - Variable in class etomica.modules.swmd.SwmdGraphic
Tuple3f - Class in org.jmol.util: A generic 3 element tuple that is represented by single precision floating point x,y and z coordinates.
Tuple3f() - Constructor for class org.jmol.util.Tuple3f
Tuple3i - Class in org.jmol.util: A 3-element tuple represented by signed integer x,y,z coordinates.
Tuple3i() - Constructor for class org.jmol.util.Tuple3i: Constructs and initializes a Tuple3i to (0,0,0).
Tuple4f - Class in org.jmol.util: A generic 4 element tuple that is represented by single precision floating point x,y,z and w coordinates.
Tuple4f() - Constructor for class org.jmol.util.Tuple4f: Constructs and initializes a Tuple4f to (0,0,0,0).
tV2 - Variable in class etomica.space.BoundaryDeformablePeriodic
twicesqrt3ofhalfofthebondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
TWO_PI - Static variable in class etomica.util.Constants
tWork - Variable in class etomica.models.nitrogen.P2Nitrogen
twosqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
twosqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
type - Variable in class etomica.action.activity.ControllerEvent
Type(String, int) - Constructor for class etomica.action.activity.ControllerEvent.Type
type - Variable in class etomica.atom.Atom
type - Variable in class etomica.integrator.IntegratorEvent
type() - Method in class etomica.integrator.IntegratorEvent
Type(String) - Constructor for class etomica.integrator.IntegratorEvent.Type
type - Static variable in class org.jmol.script.Token
type1 - Variable in class etomica.data.meter.MeterRDF
type2 - Variable in class etomica.data.meter.MeterRDF
TYPE_EDGE_ANY - Static variable in interface etomica.graph.model.Metadata
TYPE_NODE_DEFAULT - Static variable in interface etomica.graph.model.Metadata
TYPE_NODE_FIELD - Static variable in interface etomica.graph.model.Metadata
TYPE_NODE_ROOT - Static variable in interface etomica.graph.model.Metadata
typeAgentManager - Variable in class etomica.integrator.IntegratorRigidIterative
typeAgentManager - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
typeAgentManager - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
typeManager - Variable in class etomica.models.co2.PNGCPM
typeOf(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
types - Variable in class etomica.potential.Potential0Lrc
types - Variable in class etomica.potential.PotentialGroup.PotentialLinker
types - Variable in class etomica.potential.PotentialMaster.PotentialLinker

U

u - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
u - Variable in class etomica.models.nitrogen.TestRotationVector
u(double) - Method in class etomica.models.rowley.P2RepRowley: The energy u.
u(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.modules.droplet.P2Cohesion
u(double) - Method in class etomica.modules.mu.P2SquareWellOneSide: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u - Variable in class etomica.normalmode.CoordinateDefinitionLeaf
u - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
u - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
u - Variable in class etomica.normalmode.IntegratorHarmonic
u - Variable in class etomica.normalmode.MCMoveHarmonic
u - Variable in class etomica.normalmode.MCMoveHarmonicStep
u(double) - Method in class etomica.normalmode.P2XOrder
u(double) - Method in class etomica.potential.P1HydrogenMielke
u(double) - Method in interface etomica.potential.P1IntraMolecular
u(double) - Method in class etomica.potential.P2Anharmonic
u(double) - Method in class etomica.potential.P2ArgonAziz1993: The energy u.
u(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003: The energy u.
u(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003: The energy u.
u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
u(double) - Method in class etomica.potential.P2DoubleWell: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.potential.P2Dreiding: harmonic oscillator
u(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
u(double) - Method in class etomica.potential.P2Electrostatic
u(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
u(double) - Method in class etomica.potential.P2Exp6: The energy u
u(double) - Method in class etomica.potential.P2Exp6Buckingham: The energy u
u(double) - Method in class etomica.potential.P2Fene
u(double) - Method in class etomica.potential.P2HardAssociation: Returns -epsilon if less than well diameter, or zero otherwise.
u(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
u(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
u(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
u(double) - Method in class etomica.potential.P2HardBond: Returns 0 if the bond is within the required distance, infinity if not.
u(double) - Method in class etomica.potential.P2HardSphere: Interaction energy of the pair.
u(double) - Method in class etomica.potential.P2Harmonic
u(double) - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
u(double) - Method in class etomica.potential.P2HePCKLJS.P2HeTI
u(double) - Method in class etomica.potential.P2HePCKLJS: The energy u.
u(double) - Method in class etomica.potential.P2HeSimplified.P2HeQFH
u(double) - Method in class etomica.potential.P2HeSimplified.P2HeTI
u(double) - Method in class etomica.potential.P2HeSimplified: The energy u.
u(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
u(double) - Method in class etomica.potential.P2Ideal: Returns zero.
u(double) - Method in class etomica.potential.P2LennardJones: The energy u.
u(double) - Method in class etomica.potential.P2LennardJonesDreiding: The energy u.
u(double) - Method in class etomica.potential.P2LJQ
u(double) - Method in class etomica.potential.P2LJQQ
u(double) - Method in class etomica.potential.P2ModifiedMorse: The energy u.
u(double) - Method in class etomica.potential.P2Morse: The energy u.
u(double) - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
u(double) - Method in class etomica.potential.P2PenetrableBond: Returns 0 if the bond is within the required distance, infinity if not.
u(double) - Method in class etomica.potential.P2PenetrableSphere: Returns epsilon if overlapping, or zero if not.
u(double) - Method in class etomica.potential.P2PenetrableSquareWell: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.potential.P2QChemInterpolated
u(double) - Method in class etomica.potential.P2SoftSphere: The energy u.
u(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
u(double) - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the energy of the wrapped potential if the separation is less than the cutoff value
u(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted
u(double) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted: Returns the energy of the wrapped potential if the separation is less than the cutoff value
u(double) - Method in class etomica.potential.P2SoftTruncated
u(double) - Method in class etomica.potential.P2SquareWell: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.potential.P2SquareWellRobust: Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
u(double) - Method in class etomica.potential.P2Tether: Returns infinity if separation is greater than tether distance, zero otherwise
u(double) - Method in class etomica.potential.P2WCA: The energy u.
u(double) - Method in class etomica.potential.Potential2HardSpherical: The pair energy u(r^2) with no truncation applied.
u(double) - Method in interface etomica.potential.Potential2Spherical: The pair energy u(r^2) with no truncation applied.
u(double) - Method in class etomica.virial.P1IntraLambda
u(double) - Method in class etomica.yukawa.P2HC2Yukawa: Energy method.
u(double) - Method in class etomica.yukawa.P2Yukawa: Energy method.
u0 - Variable in class etomica.virial.P1IntraLambda
UAlpha(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
uBeads - Variable in class etomica.virial.PotentialGroup3PI
uBeads - Variable in class etomica.virial.PotentialGroupPI
UBeta(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
uBondCorr() - Method in class etomica.potential.EwaldSummation
uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
uCorrect - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
uCorrect - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
uCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc: Long-range correction to the energy.
uFac - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
uFcc(double, double) - Static method in class etomica.statmech.LennardJones: Total ensemble-averaged internal potential energy for the fcc solid.
uFourier() - Method in class etomica.potential.EwaldSummation
uFourier() - Method in class etomica.potential.EwaldSumMolecules
uHarmonicNew - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
uHarmonicOld - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
uijPol - Variable in class etomica.virial.ClusterSumPolarizable
uijPol - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
uijPol - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
uijPol - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
uInt(double) - Method in class etomica.models.rowley.P2RepRowley: Integral of the potential, used to evaluate corrections for potential truncation.
uInt(double) - Method in class etomica.modules.droplet.P2Cohesion
uInt(double) - Method in class etomica.potential.P2Anharmonic: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2ArgonAziz1993: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
uInt(double) - Method in class etomica.potential.P2Dreiding: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2Electrostatic
uInt(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
uInt(double) - Method in class etomica.potential.P2Exp6: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2Exp6Buckingham: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2Fene: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2Harmonic: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2HePCKLJS: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2HeSimplified: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
uInt(double) - Method in class etomica.potential.P2LennardJones: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2LennardJonesDreiding: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2LJQQ
uInt(double) - Method in class etomica.potential.P2ModifiedMorse: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2Morse: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2QChemInterpolated: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2SoftSphere: Integral used for corrections to potential truncation.
uInt(double) - Method in class etomica.potential.P2SoftSphericalTruncated: Returns the value of uInt for the wrapped potential.
uInt(double) - Method in class etomica.potential.P2WCA: Returns zero, since there is no long-range correction.
uInt(double) - Method in class etomica.potential.Potential2SoftSpherical: Integral of the potential, used to evaluate corrections for potential truncation.
uInt(double) - Method in class etomica.yukawa.P2HC2Yukawa: Integral from rC to infinity.
uInt(double) - Method in class etomica.yukawa.P2Yukawa: Integral from rC to infinity.
uisString(String) - Static method in class etomica.units.Lister
ULat - Variable in class etomica.normalmode.MeterSolidProps
ULat - Variable in class etomica.normalmode.MeterSolidPropsLJ
uLat0 - Static variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled: Nominal function for lattice energy
uLat0 - Static variable in class etomica.normalmode.MCMoveVolumeSolid: Nominal function for lattice energy
uLat0 - Static variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular: Nominal function for lattice energy
uLat0 - Static variable in class etomica.normalmode.MeterDDP: Nominal function for lattice energy
uLat0 - Static variable in class etomica.normalmode.MeterDP: Nominal function for lattice energy
ulat0 - Variable in class etomica.normalmode.SoftSphereSolidEOS
ulat0 - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
uLatFunction - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
uLatFunction - Variable in class etomica.normalmode.MCMoveVolumeSolid
uLatFunction - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
uLatFunction - Variable in class etomica.normalmode.MeterDDP
uLatFunction - Variable in class etomica.normalmode.MeterDP
ulatMeasured - Variable in class etomica.normalmode.MeterBoltzmann
ulatSampled - Variable in class etomica.normalmode.MeterBoltzmann
uLatTruncFunction - Variable in class etomica.normalmode.MCMoveVolumeSolid
ULLMAN_ALGORITHM - Static variable in interface etomica.graph.isomorphism.SearchState
UllmanSearchState - Class in etomica.graph.isomorphism
UllmanSearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.UllmanSearchState
UllmanSearchState(UllmanSearchState) - Constructor for class etomica.graph.isomorphism.UllmanSearchState
umax - Variable in class etomica.modules.clustergenerator.Plot
umin - Variable in class etomica.modules.clustergenerator.Plot
una - Variable in class etomica.virial.PotentialNonAdditive
Unary - Interface in etomica.graph.operations
UNARY_OP_EDIF - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_EXP - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_INT - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_ISO - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_NCOPY - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_NDIF - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_PCOPY - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_POWER - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_RELABEL - Static variable in interface etomica.graph.engine.Parser
UNARY_OP_SPLIT - Static variable in interface etomica.graph.engine.Parser
UnaryChain - Class in etomica.graph.operations: Facilitates a chain of unary operations.
UnaryChain(Unary, Unary) - Constructor for class etomica.graph.operations.UnaryChain
UnaryChain.ChainParameters - Class in etomica.graph.operations
UnaryOpByteImpl - Class in etomica.graph.engine.impl
UnaryOpByteImpl(String, Parser.Expression, byte) - Constructor for class etomica.graph.engine.impl.UnaryOpByteImpl
UnaryOpByteMapImpl - Class in etomica.graph.engine.impl
UnaryOpByteMapImpl(String, Parser.Expression, Map<Byte, Byte>) - Constructor for class etomica.graph.engine.impl.UnaryOpByteMapImpl
UnaryOpColorImpl - Class in etomica.graph.engine.impl
UnaryOpColorImpl(String, Parser.Expression, char) - Constructor for class etomica.graph.engine.impl.UnaryOpColorImpl
UnaryOpImpl - Class in etomica.graph.engine.impl
UnaryOpImpl(String, Parser.Expression) - Constructor for class etomica.graph.engine.impl.UnaryOpImpl
UnaryOpThreeColorImpl - Class in etomica.graph.engine.impl
UnaryOpThreeColorImpl(String, Parser.Expression, char, char, char) - Constructor for class etomica.graph.engine.impl.UnaryOpThreeColorImpl
UnaryOpTwoByteImpl - Class in etomica.graph.engine.impl
UnaryOpTwoByteImpl(String, Parser.Expression, byte, byte) - Constructor for class etomica.graph.engine.impl.UnaryOpTwoByteImpl
unbond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded: this function unbonds two atoms
Undefined - Class in etomica.units: Undefined dimension used for quantities with undefined or unknown dimensions.
undisplayThread - Variable in class etomica.modules.droplet.EllipseDisplayAction
undo() - Method in class etomica.action.BoxInflate: Reverses the action of the inflation by performing the action with a scale given the by the reciprocal of the current scale.
undo() - Method in class etomica.action.BoxInflateAnisotropic
undo() - Method in interface etomica.action.Undoable: Causes the effect of most recent call to actionPerformed to be reversed.
undo - Static variable in class org.jmol.script.Token
Undoable - Interface in etomica.action: Interface for an action that can be "undone", such that its effect is reversed if the undo() method is invoked immediately after the actionPerformed().
undomove - Static variable in class org.jmol.script.Token
unescapeBitset(String) - Static method in class org.jmol.util.Escape
unEscapeBitSetArray(BitSet) - Method in class org.jmol.script.ScriptVariable
unEscapeBitSetArray(ArrayList<ScriptVariable>, boolean) - Static method in class org.jmol.script.ScriptVariable
unescapeMatrix(String) - Static method in class org.jmol.util.Escape
unescapePoint(String) - Static method in class org.jmol.util.Escape
unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.ScriptVariable
unescapePointOrBitsetOrMatrixOrArray(String) - Static method in class org.jmol.util.Escape
unescapeStringArray(String) - Static method in class org.jmol.util.Escape
unescapeUnicode(String) - Static method in class org.jmol.util.Escape
uNew - Variable in class etomica.association.MCMoveDimer
uNew - Variable in class etomica.association.MCMoveDimerRotate
uNew - Variable in class etomica.association.MCMoveSmer
uNew - Variable in class etomica.association.MCMoveSmerRotate
uNew - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
uNew - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
uNew - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
uNew - Variable in class etomica.integrator.mcmove.MCMoveAtom
uNew - Variable in class etomica.integrator.mcmove.MCMoveDimer
uNew - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
uNew - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
uNew - Variable in class etomica.integrator.mcmove.MCMoveMolecule
uNew - Variable in class etomica.integrator.mcmove.MCMoveVolume
uNew - Variable in class etomica.models.hexane.MCMoveCBMC
uNew - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
uNew - Variable in class etomica.models.hexane.MCMoveReptate
uNew - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
uNew - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
uNew - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
uNew - Variable in class etomica.normalmode.MCMoveAtomCoupled
uNew - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
uNew - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
uNew - Variable in class etomica.normalmode.MCMoveAtomSuperBox
uNew - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
uNew - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
uNew - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
uNew - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
uNew - Variable in class etomica.spin.MCMoveSpinFlip
uNew - Variable in class etomica.virial.MCMoveClusterAngleBend
uNew - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
uNew - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
uNew - Variable in class etomica.virial.MCMoveClusterRingScale
uNewPE - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
Unfactor - Class in etomica.graph.operations: This operation will do the reverse of the Factor operation.
Unfactor() - Constructor for class etomica.graph.operations.Unfactor
Union - Class in etomica.graph.operations
Union() - Constructor for class etomica.graph.operations.Union
unit - Variable in class etomica.graphics.Device
unit - Variable in class etomica.graphics.DisplayTextBox: Physical units associated with the displayed value.
UNIT - Static variable in class etomica.units.Ampere: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Angstrom: Singleton instance of this unit
UNIT - Static variable in class etomica.units.Bar: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Barye: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.BohrRadius: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Calorie: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Candela: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Coulomb: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Count: Singleton instance of this unit
UNIT - Static variable in class etomica.units.CubicCentimeter: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.CubicMeter: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Dalton: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Debye: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Decimal: Singleton instance of this unit
UNIT - Static variable in class etomica.units.Degree: Single instance of this unit.
UNIT - Static variable in class etomica.units.Dyne: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Electron: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.ElectronVolt: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Erg: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Gram: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Hartree: Hartree unit of energy, corresponding to the approximate energy of hydrogen in its ground state.
UNIT - Static variable in class etomica.units.Joule: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Kelvin: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Liter: Singleton instance of this class.
UNIT - Static variable in class etomica.units.Meter: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Mole: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Newton: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Null: Unit for an otherwise unspecified dimensionless quantity.
UNIT - Static variable in class etomica.units.Pascal: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Percent: Singleton instance of this unit
UNIT - Static variable in class etomica.units.Picosecond: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Poise: Singleton instance of this unit.
unit() - Method in class etomica.units.PrefixedUnit: Returns the base baseUnit of the baseUnit.
UNIT - Static variable in class etomica.units.Radian: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Second: Singleton instance of this unit.
UNIT - Static variable in class etomica.units.Statcoulomb: Convenience instance of this unit to permit unit to be assigned without creating a new instance of it each time
UNIT - Static variable in class etomica.units.Undefined: Unit for a quantity having undefined or unknown units.
Unit - Interface in etomica.units: Interface used to specify the physical units to be used when inputting or outputting a quantity.
UNIT - Static variable in class etomica.units.Volt: Singleton instance of this unit.
unit() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
unitAxisVectors - Static variable in class org.jmol.viewer.JmolConstants
unitCell() - Method in class etomica.lattice.crystal.Primitive: Returns a the unit cell specified by this primitive.
unitCell() - Method in class etomica.lattice.crystal.PrimitiveCubic: Returns a new Square (if primitive is 2D) or Cube (if 3D) with edges given by the size of the primitive vectors.
unitCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic: Returns a new Cuboid with edges of length given by the current values of the primitive vectors.
unitCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal: Returns a new Cuboid with edges of length given by the current values of the primitive vectors.
unitCell() - Method in class etomica.lattice.crystal.PrimitiveTetragonal: Returns a new Cuboid with edges given by the lengths of the primitive vectors.
unitcell - Static variable in class org.jmol.script.Token
unitcellcolor - Static variable in class org.jmol.script.Token
unitCubePoints - Static variable in class org.jmol.util.BoxInfo
UnitFilter - Class in etomica.units
UnitFilter() - Constructor for class etomica.units.UnitFilter
UnitGraphics - Class in etomica.units
UnitGraphics() - Constructor for class etomica.units.UnitGraphics
unitList - Variable in class etomica.graphics.DisplayPlot
UnitRatio - Class in etomica.units: Class for constructing units forms as ratios of other units.
UnitRatio(Unit, Unit) - Constructor for class etomica.units.UnitRatio: Constructs the compound unit using conversion factors and labels from the constituent units.
UnitRatio(Unit, Unit, String, String) - Constructor for class etomica.units.UnitRatio
units - Variable in class etomica.graphics.DisplayTable
unitSelector() - Method in class etomica.graphics.DimensionedDoubleEditor: Returns a combo box that can be used to select the unit.
unitString() - Static method in class etomica.units.Lister
UnitSystem - Class in etomica.units.systems: Specifies a system of units.
UnitSystem() - Constructor for class etomica.units.systems.UnitSystem
UnitSystem.Sim - Class in etomica.units.systems: System of units based on simulation units of Daltons, picoseconds, and Angstroms
unitSystemString() - Static method in class etomica.units.Lister
unitx - Static variable in class org.jmol.script.Token
unitxyz - Static variable in class org.jmol.script.Token
unity - Static variable in class org.jmol.script.Token
unitz - Static variable in class org.jmol.script.Token
UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.Colix
unPause() - Method in class etomica.action.activity.ActivityGroupParallel
unPause() - Method in class etomica.action.activity.ActivityGroupSeries: Removes activity group from the paused state, resuming execution where it left off.
unPause() - Method in class etomica.action.Activity: Removes activity from the paused state, resuming execution where it left off.
unsafe() - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
unsafe() - Method in class etomica.modules.render.RenderMD.CriterionCar
unsafe() - Method in class etomica.modules.sam.CriterionTether3
unsafe() - Method in class etomica.nbr.CriterionAdapter: Indicates whether the atom has changed (e.g.
unsafe() - Method in class etomica.nbr.CriterionAll: Always returns false, indicating that neighbor list never needs updating.
unsafe() - Method in class etomica.nbr.CriterionNone: Always returns false, indicating that neighbor list never needs updating.
unsafe() - Method in class etomica.nbr.CriterionPositionWall
unsafe() - Method in class etomica.nbr.CriterionSimple
unsafe() - Method in class etomica.nbr.molecule.CriterionAdapterMolecular: Indicates whether the atom has changed (e.g.
unsafe() - Method in class etomica.nbr.molecule.CriterionAllMolecular: Always returns false, indicating that neighbor list never needs updating.
unsafe() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
unsafe() - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular: Indicates whether the molecule has changed (e.g.
unsafe() - Method in interface etomica.nbr.NeighborCriterion: Indicates whether the atom has changed (e.g.
unscaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociated
unscaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
unscreenedCount - Variable in class etomica.virial.MeterVirialBDBin
unscreenedCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
unscreenedCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
unscreenedCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
unseenNeighbor(byte, byte) - Method in class etomica.graph.traversal.AbstractTraversal
unset() - Method in class etomica.atom.iterator.ANIntergroupCoupled
unset() - Method in class etomica.atom.iterator.ANIntergroupExchange
unset() - Method in class etomica.atom.iterator.ANIntragroupExchange
unset() - Method in class etomica.atom.iterator.ApiIndexList: Sets iterator to a state where hasNext() returns false.
unset() - Method in class etomica.atom.iterator.ApiInnerVariable: Sets the iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.ApiInterArrayList: Sets iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.ApiIntergroup: Sets the iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.ApiIntraArrayList: Sets iterator such that next is null.
unset() - Method in class etomica.atom.iterator.ApiIntragroup
unset() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
unset() - Method in class etomica.atom.iterator.AtomIteratorArrayList
unset() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent: Puts iterator in a state where hasNext is false.
unset() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple: Puts iterator in state in which hasNext is false.
unset() - Method in class etomica.atom.iterator.AtomIteratorNull
unset() - Method in class etomica.atom.iterator.AtomIteratorSinglet: Sets iterator to a state where hasNext() returns false.
unset() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList: Sets iterator to a state where hasNext() returns false.
unset() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList: Sets iterator to a state where hasNext() returns false.
unset() - Method in interface etomica.atom.iterator.AtomsetIterator: Puts iterator in a state in which hasNext() returns false.
unset() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
unset() - Method in class etomica.atom.iterator.MoleculeIteratorAll
unset() - Method in class etomica.atom.iterator.MoleculeIteratorArrayList
unset() - Method in class etomica.atom.iterator.MoleculeIteratorArrayListSimple: Puts iterator in state in which hasNext is false.
unset() - Method in class etomica.atom.iterator.MoleculeIteratorSinglet: Sets iterator to a state where hasNext() returns false.
unset() - Method in class etomica.atom.iterator.MpiInnerFixed: Sets the iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.MpiInnerVariable: Sets the iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.MpiInterArrayList: Sets iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.MpiInterspecies1A
unset() - Method in class etomica.atom.iterator.MpiInterspeciesAA: Sets iterator such that hasNext is false.
unset() - Method in class etomica.atom.iterator.MpiIntraArrayList: Sets iterator such that next is null.
unset() - Method in class etomica.atom.iterator.MpiIntraspecies1A
unset() - Method in class etomica.atom.iterator.MpiIntraspeciesAA: Sets iterator such that next is null.
unset() - Method in class etomica.atom.iterator.MpiMolecule: Sets iterator to state in which hasNext is false.
unset() - Method in class etomica.atom.iterator.TripletInnerSequential
unset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
unset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
unset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
unset() - Method in class etomica.lattice.RectangularLattice.Iterator
unset() - Method in class etomica.lattice.RectangularLatticeNbrIterator: Puts iterator in a state in which hasNext() returns false.
unset() - Method in interface etomica.lattice.SiteIterator: Puts the iterator in a state such that hasNext is false.
unset() - Method in class etomica.nbr.cell.Api1ACell
unset() - Method in class etomica.nbr.cell.ApiAACell
unset() - Method in class etomica.nbr.cell.AtomIteratorCell
unset() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
unset() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
unset() - Method in class etomica.nbr.cell.molecule.MpiAACell
unset() - Method in class etomica.nbr.site.Api1ASite
unset() - Method in class etomica.potential.PotentialMaster.AtomIterator0
unset() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
uOld - Variable in class etomica.association.MCMoveDimer
uOld - Variable in class etomica.association.MCMoveDimerRotate
uOld - Variable in class etomica.association.MCMoveSmer
uOld - Variable in class etomica.association.MCMoveSmerRotate
uOld - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
uOld - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
uOld - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
uOld - Variable in class etomica.integrator.mcmove.MCMoveAtom
uOld - Variable in class etomica.integrator.mcmove.MCMoveDimer
uOld - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
uOld - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
uOld - Variable in class etomica.integrator.mcmove.MCMoveMolecule
uOld - Variable in class etomica.integrator.mcmove.MCMoveVolume
uOld - Variable in class etomica.models.hexane.MCMoveCBMC
uOld - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
uOld - Variable in class etomica.models.hexane.MCMoveReptate
uOld - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
uOld - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
uOld - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
uOld - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
uOld - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
uOld - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
uOld - Variable in class etomica.normalmode.IntegratorHarmonic
uOld - Variable in class etomica.normalmode.MCMoveAtomCoupled
uOld - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
uOld - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
uOld - Variable in class etomica.normalmode.MCMoveAtomSuperBox
uOld - Variable in class etomica.normalmode.MCMoveHarmonic
uOld - Variable in class etomica.normalmode.MCMoveHarmonicStep
uOld - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
uOld - Variable in class etomica.normalmode.MCMoveSingleMode
uOld - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
uOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
uOld - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
uOld - Variable in class etomica.spin.MCMoveSpinFlip
uOld - Variable in class etomica.virial.MCMoveClusterAngleBend
uOld - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
uOld - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
uOld - Variable in class etomica.virial.MCMoveClusterRingScale
uOldPE - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
UP - Static variable in class etomica.atom.iterator.IteratorDirective.Direction
uPair - Variable in class etomica.virial.PotentialCommonAtomic
update() - Method in class etomica.data.DataSourceFunction: Updates the wrapped Data and DataInfo for change to the xDataSource
update(double[][], DataDoubleArray.DataInfoDoubleArray[]) - Method in class etomica.data.DataSourceIndependentSimple
update(double[], DataDoubleArray.DataInfoDoubleArray) - Method in class etomica.data.DataSourceIndependentSimple
update(double[], double[]) - Method in class etomica.data.DataSourcePoints
update(Set<Graph>) - Method in interface etomica.graph.engine.Viewer
update(Set<Graph>) - Method in class etomica.graph.viewer.ClusterViewer
update() - Method in class etomica.lattice.crystal.Primitive
update() - Method in class etomica.lattice.crystal.PrimitiveBcc
update() - Method in class etomica.lattice.crystal.PrimitiveCubic
update() - Method in class etomica.lattice.crystal.PrimitiveFcc
update() - Method in class etomica.lattice.crystal.PrimitiveGeneral
update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal.PrimitiveHexagonalReciprocal
update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
update() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
update() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
update() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
update() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
update() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
update() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
update() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
update() - Method in class etomica.models.hexane.PrimitiveHexane
update(Graphics) - Method in class etomica.modules.clustergenerator.Plot
update() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
update(BravaisLattice) - Method in class etomica.modules.crystalviewer.CrystalViewer
update() - Method in class etomica.modules.crystalviewer.LatticeEditor
update() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
update() - Method in class etomica.space.BoundaryDeformablePeriodic
update(Graphics) - Method in class etomica.util.Grabber.ImagePanel
updateAtom(IAtom) - Method in class etomica.integrator.IntegratorHard: updates collision time for a single atom (and any atom that might a collision with the atom)
updateAtom(IAtom) - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
updateAtoms(AtomPair) - Method in class etomica.integrator.IntegratorHard: Updates collision times/partners for collider and partner, and for atoms that were to collide with one of them.
updateBegin() - Method in interface etomica.graph.engine.Console
updateBegin() - Method in class etomica.graph.engine.ConsoleUI
updateConformation(int) - Method in class etomica.modules.sam.Sam
updateCounts(boolean, double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
updateCounts(boolean, double) - Method in class etomica.integrator.mcmove.MCMoveTracker: Updates statistics regarding the acceptance rate of this move.
updateDataMap() - Method in class etomica.data.DataSet: This updates the mapping between pseudo DataSinks and indices (used for getData(int), etc.).
updateDimensions() - Method in class etomica.space.BoundaryRectangular
updateDimensions() - Method in class etomica.space.BoundaryRectangularPeriodic
updateDimensions() - Method in class etomica.space.BoundaryRectangularPore
updateDimensions() - Method in class etomica.space.BoundaryRectangularSlit
updateDone() - Method in interface etomica.graph.engine.Console
updateDone() - Method in class etomica.graph.engine.ConsoleUI
updateDrawType() - Method in class g3dsys.images.ImageShell: Updates line-drawing status depending on whether images are on and the current draw boundary type.
updateEditor() - Method in class etomica.graphics.PropertyText
updateF() - Method in class etomica.data.DataSourceFunction
updateF(BoxCluster) - Method in class etomica.virial.ClusterChainHS
updateF(BoxCluster) - Method in class etomica.virial.ClusterChainSoft
updateF(BoxCluster) - Method in class etomica.virial.ClusterSinglyConnected
updateF(BoxCluster) - Method in class etomica.virial.ClusterSum
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumEF
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumHS
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumMultibody
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumMultibodyShell
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
updateF(BoxCluster) - Method in class etomica.virial.ClusterSumShell
updateF(CoordinatePairSet, AtomPairSet) - Method in class etomica.virial.ClusterTree
updateF(CoordinatePairLeafSet, AtomPairSet) - Method in class etomica.virial.ClusterTreeEF
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS.AllSigs
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
updateF() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBDMix
updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftMix
updateFlowLines() - Method in class etomica.modules.rheology.RheologyGraphic
updateIntegrator() - Method in class etomica.graphics.DeviceThermoSelector: set the integrator's temperature to the selected value
updateLine(int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
updateLists() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
updateLists() - Method in class etomica.nbr.list.NeighborListManager
updateMrLast() - Method in class etomica.integrator.IntegratorVerlet
updateNbrsIfNeeded() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular: Checks whether any atom needs neighbor list updating, and if one is found, performs neighbor list updates of all atom neighbor lists.
updateNbrsIfNeeded() - Method in class etomica.nbr.list.NeighborListManager: Checks whether any atom needs neighbor list updating, and if one is found, performs neighbor list updates of all atom neighbor lists.
updateNeighborList() - Method in class etomica.lattice.RectangularLatticeNbrIterator
updateNeighborList() - Method in class etomica.lattice.RectangularLatticeNbrIteratorAdjacent
updateNeighborList() - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare: Method called on reset if any calls were previously made to setLattice, setSite, setRange, or setDirection.
updateNewMoleculePair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
updateNewMoleculePair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
updatePiston() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston: recalculate collision times for all atoms with the wall/piston
updatePlane(int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
updateQuaternion() - Method in class etomica.math.Quaternion: First checks if all the components are numbers.
updateRCut() - Method in class etomica.modules.sam.Sam
updateVertices() - Method in class etomica.math.geometry.Cube
updateVertices() - Method in class etomica.math.geometry.Cuboid
updateVertices() - Method in class etomica.math.geometry.LineSegment
updateVertices() - Method in class etomica.math.geometry.Parallelepiped: Calculated vertices based on current values of edge vectors.
updateVertices() - Method in class etomica.math.geometry.Parallelogram: Calculated vertices based on current values of edge vectors.
updateVertices() - Method in class etomica.math.geometry.Point: Does nothing; the point is the vertex.
updateVertices() - Method in class etomica.math.geometry.PolygonGeneral
updateVertices() - Method in class etomica.math.geometry.PolyhedronGeneral: Calculates vertices from their internal representation, which for a general polyhedron does nothing because the vertices are the internal representation.
updateVertices() - Method in class etomica.math.geometry.Polytope: This method should be defined by the subclass to calculate the vertices in accordance with the internal representation of the polytope.
updateVertices() - Method in class etomica.math.geometry.Rectangle
updateVertices() - Method in class etomica.math.geometry.Square
updateVertices() - Method in class etomica.math.geometry.TruncatedOctahedron: The following defines the vertices that the truncated octahedron will have, based on Vector3D.
upList - Variable in class etomica.integrator.IntegratorHard
upList - Variable in class etomica.nbr.list.AtomNeighborLists
upList - Variable in class etomica.nbr.list.molecule.MoleculeNeighborLists
upListNow - Variable in class etomica.atom.iterator.AtomIteratorArrayList
upListNow - Variable in class etomica.atom.iterator.MoleculeIteratorArrayList
upListNow - Variable in class etomica.atom.iterator.MpiIntraspecies1A
UpolAtkins - Variable in class etomica.models.co2.PNCO2GCPM
UPPER_MASK - Static variable in class etomica.util.RandomMersenneTwister
uReactCO - Variable in class etomica.modules.catalysis.ReactionManagerCO
uReactCORev - Variable in class etomica.modules.catalysis.ReactionManagerCO
uReal() - Method in class etomica.potential.EwaldSummation
uReal() - Method in class etomica.potential.EwaldSumMolecules
urgentWaitObject - Variable in class etomica.action.activity.Controller
UrgentWaitObject() - Constructor for class etomica.action.activity.Controller.UrgentWaitObject
USAGE - Static variable in class etomica.graph.view.rasterizer.Main: Describes the command line options for the rasterizer
usage() - Static method in class etomica.util.numerical.AkimaSplineSmootherMain
uSCFData - Variable in class etomica.potential.P2QChemInterpolated
USE_PALETTE - Static variable in class org.jmol.util.Colix
usearcball - Static variable in class org.jmol.script.Token
useC10 - Static variable in class etomica.potential.P2HeSimplified
useE - Variable in class etomica.virial.PYGenerator.IteratorEF
uSelf() - Method in class etomica.potential.EwaldSummation
uSelf() - Method in class etomica.potential.EwaldSumMolecules
useminimizationthread - Static variable in class org.jmol.script.Token
useNeighborLists - Variable in class etomica.simulation.prototypes.HSMD3D.HSMD3DParam
usenumberlocalization - Static variable in class org.jmol.script.Token
usePermutations - Variable in class etomica.virial.ClusterBonds
usePhongExponent - Static variable in class org.jmol.util.Shader
usercolorscheme - Static variable in class org.jmol.script.Token
useReverseEdges - Static variable in class etomica.graph.model.impl.GraphImpl
userStylesheet - Variable in class etomica.graph.view.rasterizer.SVGConverter: User stylesheet
useSurfaceOnly - Variable in class etomica.modules.droplet.P2Cohesion
useSZ - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
useUB - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
useUB - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
Ushcats - Class in etomica.veos
Ushcats(BetaSource, int) - Constructor for class etomica.veos.Ushcats
UShift(P2SoftSphericalTruncated) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
uShift - Variable in class etomica.normalmode.SimLJVacancy
uShift - Variable in class etomica.rotation.P2LJDipole
USine(P2SoftSphericalTruncated, double[][], double) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
uStaticFcc(double) - Static method in class etomica.statmech.LennardJones: Potential energy per atom of a static fcc lattice with a LJ particle at each site.
uSums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
uTriplet - Variable in class etomica.virial.PotentialCommonAtomic
uValues - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
uValues - Variable in class etomica.virial.MCMoveClusterPolyhedraTree

V

V - Variable in class etomica.dimer.IntegratorDimerRT
v(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
v(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
v(double, double) - Method in interface etomica.mappedvirial.PotentialCalculationMappedVirialV.VFunc
v - Variable in class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
v - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
v - Variable in class etomica.nbr.cell.NeighborCellManager
v - Variable in class etomica.normalmode.HSNPT.ActionSummer
v - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
v - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
v - Variable in class etomica.potential.P2SpheroPolyhedron
v - Variable in class etomica.potential.P3HydrogenManzhos.P3HydrogenManzhosMolecular
v - Variable in class etomica.virial.IntSet
v0 - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
v0 - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
v1 - Variable in class etomica.config.ConformationChainZigZag
v1 - Variable in class etomica.config.ConformationChainZigZag2
v1 - Variable in class etomica.potential.P4BondTorsion
v1 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
v2 - Variable in class etomica.config.ConformationChainZigZag
v2 - Variable in class etomica.config.ConformationChainZigZag2
v2 - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
v2 - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
v2 - Variable in class etomica.potential.P4BondTorsion
v2 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
v2 - Variable in class etomica.space3d.OrientationFull3D
v3 - Variable in class etomica.space3d.OrientationFull3D
valence - Static variable in class org.jmol.script.Token
validate - Variable in class etomica.graph.view.rasterizer.SVGConverter: Validation flag
validateBondList(IAtom, IAtomList, boolean) - Method in class etomica.association.AssociationHelperBranched: Returns false if invalid bonding is recognized
validateBondList(IAtom, IAtomList, boolean) - Method in class etomica.association.AssociationHelperDouble
validateBondList(IMolecule, IMoleculeList, boolean) - Method in class etomica.association.AssociationHelperMolecule: Returns false if invalid bonding is recognized
validateConverterConfig(SVGConverter) - Method in class etomica.graph.view.rasterizer.Main: Template methods which subclasses may implement to do whatever is needed.
value - Variable in class etomica.compatibility.NumericFeature
value - Variable in class etomica.compatibility.StringFeature
value(Graph) - Static method in class etomica.graph.property.NumFieldNodes
value(Graph) - Static method in class etomica.graph.property.NumRootNodes
value - Variable in class etomica.graphics.DisplayTextBox: Object for displaying the value as a text field
value() - Method in class etomica.units.Prefix
value() - Method in class etomica.veos.BigValue: Returns the value held by the instance (in true form, not as log, and with sign applied).
value() - Method in interface etomica.veos.IBigValue: Returns the value held by the instance (in true form, not as log, and with sign applied).
value() - Method in class etomica.veos.MyBigDecimal: Returns the value held by the instance (in true form, not as log, and with sign applied).
value(double) - Static method in class etomica.virial.B3LJ
value(List, boolean) - Method in class etomica.virial.CalcFFT
value(double[][]) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
value(double[][]) - Method in class etomica.virial.cluster.ClusterDiagramTree
value(double[][]) - Method in class etomica.virial.cluster.ClusterTreeNode
value(BoxCluster) - Method in interface etomica.virial.ClusterAbstract: Value of this cluster for the given pairset at the specified reciprocal temperature.
value(double[][][]) - Method in class etomica.virial.ClusterBonds: Returns the value of the cluster for the given set of atom pairs at the given value of beta = 1/kT.
value(double[][][], double[][]) - Method in class etomica.virial.ClusterBondsNonAdditive
value - Variable in class etomica.virial.ClusterChainHS
value(BoxCluster) - Method in class etomica.virial.ClusterChainHS
value - Variable in class etomica.virial.ClusterChainSoft
value(BoxCluster) - Method in class etomica.virial.ClusterChainSoft
value - Variable in class etomica.virial.ClusterCoupledFlipped
value(BoxCluster) - Method in class etomica.virial.ClusterCoupledFlipped
value - Variable in class etomica.virial.ClusterCoupledFlippedPartial
value(BoxCluster) - Method in class etomica.virial.ClusterCoupledFlippedPartial
value(BoxCluster) - Method in class etomica.virial.ClusterDifference
value(BoxCluster) - Method in class etomica.virial.ClusterExchange
value - Variable in class etomica.virial.ClusterSinglyConnected
value(BoxCluster) - Method in class etomica.virial.ClusterSinglyConnected
value - Variable in class etomica.virial.ClusterSum
value(BoxCluster) - Method in class etomica.virial.ClusterSum
value(BoxCluster) - Method in class etomica.virial.ClusterSumExternalField
value(BoxCluster) - Method in class etomica.virial.ClusterSumHS
value(BoxCluster) - Method in class etomica.virial.ClusterSumIC
value(BoxCluster) - Method in class etomica.virial.ClusterSumMultibody
value(BoxCluster) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizable
value - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
value - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
value - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
value(BoxCluster) - Method in class etomica.virial.ClusterSumStickyEF
value(BoxCluster) - Method in class etomica.virial.ClusterTree
value(BoxCluster) - Method in class etomica.virial.ClusterWeightAbs
value(BoxCluster) - Method in class etomica.virial.ClusterWeightSumWall
value(BoxCluster) - Method in class etomica.virial.ClusterWeightUmbrella
value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
value - Variable in class etomica.virial.ClusterWheatleyHS
value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
value - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
value - Variable in class etomica.virial.ClusterWheatleySoft
value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
value - Variable in class etomica.virial.ClusterWheatleySoftBD
value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
value() - Method in interface etomica.virial.IntSet.PropertyBin
value(int, int[]) - Method in class etomica.virial.simulations.VirialHSBinMultiThreaded.DooDad
value - Variable in class org.jmol.script.Token
value12(int) - Method in class etomica.virial.ClusterSumIC
valueArray(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
ValueCache(DataSourceScalar, IIntegrator) - Constructor for class etomica.liquidLJ.LjMd3D.ValueCache
ValueCache - Class in etomica.liquidLJ
ValueCache(DataSourceScalar, IIntegrator) - Constructor for class etomica.liquidLJ.ValueCache
valueChanged(ListSelectionEvent) - Method in class etomica.veos.bigdecimal.Wigner3jGUI: Interpreter parser loop.
valueClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
valueEditor() - Method in class etomica.graphics.DimensionedDoubleEditor
valueForSig(long) - Method in class etomica.virial.ClusterWheatleyHS.AllSigs
ValueImpl - Class in etomica.graph.engine.impl
ValueImpl(String) - Constructor for class etomica.graph.engine.impl.ValueImpl
valueOf(String) - Static method in enum etomica.models.co2.P2CO2Hellmann.Parameters: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.models.co2.PNCO2GCPM.Component: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.models.co2.PNGCPM.Component: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.models.water.P2WaterSzalewicz.Component: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.parser.ParserLAMMPS.Truncation: Returns the enum constant of this type with the specified name.
valueOf(Vector<BigInteger>, BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath: Evaluate the value of an integer polynomial at some integer argument.
valueOf(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Evaluate at some integer argument.
valueOf(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly: Horner scheme to find the function value at the argument x
valueOf(String) - Static method in enum etomica.virial.GUI.models.EnumPotentialParamDescription: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.virial.GUI.models.EnumSiteName: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.virial.simulations.VirialHePI.FlexApproach: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.virial.simulations.VirialHSOrC.PotentialChoice: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum etomica.virial.simulations.VirialLJOrC.PotentialChoice: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumPalette: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumStereoMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jmol.constant.EnumVdw: Returns the enum constant of this type with the specified name.
values() - Static method in enum etomica.models.co2.P2CO2Hellmann.Parameters: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.models.co2.PNCO2GCPM.Component: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.models.co2.PNGCPM.Component: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.models.water.P2WaterSzalewicz.Component: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.parser.ParserLAMMPS.Truncation: Returns an array containing the constants of this enum type, in the order they are declared.
values - Static variable in class etomica.potential.P2WaterPotentialsJankowski
values() - Static method in enum etomica.virial.GUI.models.EnumPotentialParamDescription: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.virial.GUI.models.EnumSiteName: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.virial.simulations.VirialHePI.FlexApproach: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.virial.simulations.VirialHSOrC.PotentialChoice: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum etomica.virial.simulations.VirialLJOrC.PotentialChoice: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumPalette: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumStereoMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jmol.constant.EnumVdw: Returns an array containing the constants of this enum type, in the order they are declared.
valueUsingPermutations(double[][][]) - Method in class etomica.virial.ClusterBonds: Returns value obtained by averaging over all unique permutations of the point indices.
VanderWaals - Class in etomica.veos
VanderWaals(double) - Constructor for class etomica.veos.VanderWaals
VanderWaals(double, int) - Constructor for class etomica.veos.VanderWaals
vanderwaals - Static variable in class org.jmol.script.Token
vanderwaalsMars - Static variable in class org.jmol.util.Elements: Default table of van der Waals Radii.
vaporColor - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
vaporFccCoexDensities(double) - Static method in class etomica.statmech.LennardJones: Returns the densities of coexisting (saturated) vapor and fcc phases (sublimation densities).
vaporFccCoexPressure(double) - Static method in class etomica.statmech.LennardJones: Returns the saturation pressure for vapor-fcc coexistence.
VariableImpl - Class in etomica.graph.engine.impl
VariableImpl(String) - Constructor for class etomica.graph.engine.impl.VariableImpl
Variables() - Constructor for class etomica.util.OdeSolver.Variables
Variables(int) - Constructor for class etomica.util.OdeSolver.Variables
Variables(double, double[]) - Constructor for class etomica.util.OdeSolver.Variables
Variables(OdeSolver.Variables) - Constructor for class etomica.util.OdeSolver.Variables
vBias - Variable in class etomica.integrator.mcmove.MCMoveVolume
vBias - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
vBias - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
vCO - Variable in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
vCO - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
vCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
vCut - Variable in class etomica.mappedvirial.MappedUpotential
vCut - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
vCut - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
vCut2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
vCut2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
vDataSource - Variable in class etomica.data.meter.MeterPressureByVolumeChange
VdwPROBE - Static variable in class org.jmol.util.Elements
vec - Variable in class etomica.math.Quaternion
vec - Variable in class etomica.potential.P3HydrogenManzhos
vector - Variable in class etomica.data.DataSourceAtomDistance
vector - Variable in class etomica.models.nitrogen.ConformationNitrogen
vector - Variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
vector - Variable in class etomica.virial.Conformation7SiteRigidSF6
vector - Variable in class etomica.virial.ConformationAnthracene3site
vector - Variable in class etomica.virial.ConformationAnthraceneTraPPE
vector - Variable in class etomica.virial.ConformationCO2
vector - Variable in class etomica.virial.ConformationNaphthaleneTraPPE
vector - Variable in class etomica.virial.ConformationPh3site
vector - Variable in class etomica.virial.ConformationPhenanthreneTraPPE
vector - Static variable in class org.jmol.script.Token
vector1 - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
Vector1D - Class in etomica.space1d: Implementation of the Vector class for a 1-dimensional space.
Vector1D() - Constructor for class etomica.space1d.Vector1D
Vector1D(double) - Constructor for class etomica.space1d.Vector1D
Vector1D(double[]) - Constructor for class etomica.space1d.Vector1D
Vector1D(Vector1D) - Constructor for class etomica.space1d.Vector1D
vector2 - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
Vector2D - Class in etomica.space2d: Implementation of the Vector class for a 2-dimensional space.
Vector2D() - Constructor for class etomica.space2d.Vector2D
Vector2D(double, double) - Constructor for class etomica.space2d.Vector2D
Vector2D(double[]) - Constructor for class etomica.space2d.Vector2D
Vector2D(Vector2D) - Constructor for class etomica.space2d.Vector2D
Vector3D - Class in etomica.space3d: Implementation of the Vector class for a 3-dimensional space.
Vector3D() - Constructor for class etomica.space3d.Vector3D
Vector3D(double, double, double) - Constructor for class etomica.space3d.Vector3D
Vector3D(double[]) - Constructor for class etomica.space3d.Vector3D
Vector3D(Vector3D) - Constructor for class etomica.space3d.Vector3D
Vector3f - Class in org.jmol.util: A 3-element vector that is represented by single precision floating point x,y,z coordinates.
Vector3f() - Constructor for class org.jmol.util.Vector3f
VectorForce(ISpace) - Constructor for class etomica.normalmode.LJVacancyMin.VectorForce
VectorND - Class in etomica.spaceNd: Implementation of the Vector class for a 3-dimensional space.
VectorND(int) - Constructor for class etomica.spaceNd.VectorND
VectorND(double[]) - Constructor for class etomica.spaceNd.VectorND
vectorR - Variable in class etomica.models.nitrogen.P2Nitrogen
vectors - Variable in class etomica.config.ConformationChain2D
vectors() - Method in class etomica.lattice.crystal.Primitive: Returns the primitive vectors.
vectors - Variable in class org.jmol.util.Quadric
vectorscale - Static variable in class org.jmol.script.Token
VectorSource(ISpace) - Constructor for class etomica.integrator.IntegratorMD.VectorSource
vectorsymmetry - Static variable in class org.jmol.script.Token
vEHS - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
velocity - Variable in class etomica.atom.AtomLeafDynamic
velocity - Variable in class etomica.atom.MoleculeOrientedDynamic
VELOCITY_SCALING - Static variable in class etomica.integrator.IntegratorMD.ThermostatType
velocityButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
VEOS3SW - Class in etomica.modules.adsorption
VEOS3SW() - Constructor for class etomica.modules.adsorption.VEOS3SW
verbose - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
verbose - Variable in class etomica.potential.P3CPSNonAdditiveHe
verbose - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
verbose - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
verbose - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
verbose - Variable in class etomica.util.numerical.NewtonMinimization
verbose - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
Verlet() - Method in class etomica.threads.ThreadsMD
version - Static variable in class org.jmol.viewer.JmolConstants
vertexColixes - Variable in class org.jmol.util.MeshSurface
vertexCount - Variable in class org.jmol.util.MeshSurface
vertexCount0 - Variable in class org.jmol.util.MeshSurface
vertexSets - Variable in class org.jmol.util.MeshSurface
vertexSource - Variable in class org.jmol.util.MeshSurface
vertexValues - Variable in class org.jmol.util.MeshSurface
VERTICAL - Static variable in class etomica.util.Constants.Alignment
vertices - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
vertices - Variable in class etomica.math.geometry.Polytope: These vertices are used in all external representations of the polygon.
vertices - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
vertices - Variable in class org.jmol.util.MeshSurface
vf - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
VF2_ALGORITHM - Static variable in interface etomica.graph.isomorphism.SearchState
VF2SearchState - Class in etomica.graph.isomorphism
VF2SearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.VF2SearchState
VF2SearchState(VF2SearchState) - Constructor for class etomica.graph.isomorphism.VF2SearchState
VF_ALGORITHM - Static variable in interface etomica.graph.isomorphism.SearchState
VFSearchState - Class in etomica.graph.isomorphism
VFSearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.VFSearchState
VFSearchState(VFSearchState) - Constructor for class etomica.graph.isomorphism.VFSearchState
vH2H2(double, double, double, double, double, double) - Method in class etomica.potential.P2HydrogenHinde
vH2H2(double, double, double, double, double, double) - Method in class etomica.potential.P2HydrogenHindeAtomic
vH2H2(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
vH2H2(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
vH2H2H2(IVectorMutable[]) - Method in class etomica.potential.P3HydrogenManzhos
vhs - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
vhs - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
vib - Variable in class etomica.dimer.IntegratorDimerMin
vib - Variable in class etomica.dimer.IntegratorDimerRT
vib0 - Variable in class etomica.normalmode.SoftSphereSolidEOS
vib0 - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
vibration - Static variable in class org.jmol.script.Token
vibrationperiod - Static variable in class org.jmol.script.Token
vibrationscale - Static variable in class org.jmol.script.Token
vibx - Static variable in class org.jmol.script.Token
vibxyz - Static variable in class org.jmol.script.Token
viby - Static variable in class org.jmol.script.Token
vibz - Static variable in class org.jmol.script.Token
ViewAlertMsgBox - Class in etomica.virial.GUI.views
ViewAlertMsgBox(String) - Constructor for class etomica.virial.GUI.views.ViewAlertMsgBox
ViewAlertMsgBoxSpeciesRemoval - Class in etomica.virial.GUI.views
ViewAlertMsgBoxSpeciesRemoval(String) - Constructor for class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
ViewAlkaneLengthSelection - Class in etomica.virial.GUI.views
ViewAlkaneLengthSelection(String) - Constructor for class etomica.virial.GUI.views.ViewAlkaneLengthSelection
ViewConsoleOutputBox - Class in etomica.virial.GUI.views
ViewConsoleOutputBox() - Constructor for class etomica.virial.GUI.views.ViewConsoleOutputBox
Viewer - Interface in etomica.graph.engine
viewer - Variable in class etomica.modules.crystalviewer.LatticeEditor
ViewSimEnvironmentSelection - Class in etomica.virial.GUI.views
ViewSimEnvironmentSelection(ModelSimulationEnvironment) - Constructor for class etomica.virial.GUI.views.ViewSimEnvironmentSelection
ViewSpeciesSelection - Class in etomica.virial.GUI.models
ViewSpeciesSelection(ModelSpeciesSelection, ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.models.ViewSpeciesSelection
ViewSpeciesSelection - Class in etomica.virial.GUI.views
ViewSpeciesSelection(ModelSpeciesSelection, ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.views.ViewSpeciesSelection
virial(IAtomList) - Method in class etomica.dimer.P1LepsHarmonic
virial(IAtomList) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
virial(IAtomList) - Method in class etomica.interfacial.P1Wall
virial - Variable in class etomica.liquidLJ.MeterPU
virial(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti: Virial of the pair as given by the du(double) method
virial(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat: Virial of the pair as given by the du(double) method
virial(IAtomList) - Method in class etomica.meam.PotentialCuLREP
virial(IAtomList) - Method in class etomica.meam.PotentialEFS
virial(IAtomList) - Method in class etomica.meam.PotentialFeEAM
virial(IAtomList) - Method in class etomica.meam.PotentialFeEAM_LS
virial(IAtomList) - Method in class etomica.meam.PotentialMEAM
virial(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
virial(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
virial(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
virial(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenAB
virial(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
virial(IMoleculeList) - Method in class etomica.models.water.P2Water3PSoft
virial(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
virial(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
virial(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
virial(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
virial(IAtomList) - Method in class etomica.modules.droplet.P1Smash
virial(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
virial(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
virial(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
virial(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
virial(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
virial(IAtomList) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
virial(IAtomList) - Method in class etomica.potential.EwaldSummation
virial(IAtomList) - Method in class etomica.potential.P1Harmonic
virial(IAtomList) - Method in class etomica.potential.P1HarmonicSite
virial(IAtomList) - Method in class etomica.potential.P1SoftBoundary
virial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
virial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSites
virial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeOneSite
virial(IMoleculeList) - Method in class etomica.potential.P2HSDipole
virial(IAtomList) - Method in class etomica.potential.P2Ideal: Returns zero.
virial(IMoleculeList) - Method in class etomica.potential.P2LJDipole
virial(IAtomList) - Method in class etomica.potential.P2LJQ
virial(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
virial(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole.P0ReactionField
virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
virial(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
virial(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
virial(IAtomList) - Method in class etomica.potential.P2SoftTruncated: Returns the 2nd derivative (r^2 d^2u/dr^2) of the wrapped potential if the separation is less than the cutoff value
virial(IAtomList) - Method in class etomica.potential.P3BondAngle
virial(IAtomList) - Method in class etomica.potential.P3BondAngleDreiding
virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHe
virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
virial(IAtomList) - Method in class etomica.potential.P4BondTorsion
virial(IAtomList) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
virial(IAtomList) - Method in class etomica.potential.P4BondTorsionOPLS
virial(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
virial(IAtomList) - Method in class etomica.potential.Potential2SoftSpherical: Virial of the pair as given by the du(double) method
virial(IAtomList) - Method in class etomica.potential.Potential2SoftSphericalLS: Virial of the pair as given by the du(double) method
virial(IMoleculeList) - Method in class etomica.potential.PotentialGroupSoft
virial(IMoleculeList) - Method in interface etomica.potential.PotentialMolecularSoft
virial(IAtomList) - Method in interface etomica.potential.PotentialSoft
virial(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
Virial2CLJQ - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
Virial2CLJQ() - Constructor for class etomica.virial.simulations.Virial2CLJQ
Virial2CLJQ.Virial2CLJQParam - Class in etomica.virial.simulations: Inner class for parameters
Virial2CLJQParam() - Constructor for class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
Virial7SiteRigidSF6 - Class in etomica.virial.simulations: Virial coefficients calculation of SF6 7 sites LJ + rigid without Coulombic interaction Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study Mayer sampling to evaluate cluster integrals
Virial7SiteRigidSF6() - Constructor for class etomica.virial.simulations.Virial7SiteRigidSF6
Virial7SiteRigidSF6.VirialSF6Param - Class in etomica.virial.simulations: Inner class for parameters
VirialAceticAcid - Class in etomica.virial.simulations: Mayer-sampling MC simulation for acetic acid using IMPROVED OPLS united-atom model
VirialAceticAcid() - Constructor for class etomica.virial.simulations.VirialAceticAcid
VirialAceticAcid.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAceticAcidFlex - Class in etomica.virial.simulations: Mayer-sampling MC simulation for acetic acid using IMPROVED TraPPE-UA model Flexible correction is included
VirialAceticAcidFlex() - Constructor for class etomica.virial.simulations.VirialAceticAcidFlex
VirialAceticAcidFlex.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkane - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the TraPPE force field.
VirialAlkane() - Constructor for class etomica.virial.simulations.VirialAlkane
VirialAlkane.VirialSiepmannSpheresParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneEHTest - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the TraPPE-Explicit Hydrogen force field.
VirialAlkaneEHTest() - Constructor for class etomica.virial.simulations.VirialAlkaneEHTest
VirialAlkaneEHTest.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneFlex - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the TraPPE force field.
VirialAlkaneFlex() - Constructor for class etomica.virial.simulations.VirialAlkaneFlex
VirialAlkaneFlex.VirialSiepmannSpheresParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneFull - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the TraPPE-United Atoms force field.
VirialAlkaneFull() - Constructor for class etomica.virial.simulations.VirialAlkaneFull
VirialAlkaneFull.VirialSiepmannSpheresParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneMix - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the dispersion interaction.
VirialAlkaneMix() - Constructor for class etomica.virial.simulations.VirialAlkaneMix
VirialAlkaneMix.VirialAlkaneMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneMix2 - Class in etomica.virial.simulations
VirialAlkaneMix2() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2
VirialAlkaneMix2.VirialAlkaneMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneMix2_Kong - Class in etomica.virial.simulations
VirialAlkaneMix2_Kong() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2_Kong
VirialAlkaneMix2_Kong.VirialAlkaneMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneMix_Kong - Class in etomica.virial.simulations
VirialAlkaneMix_Kong() - Constructor for class etomica.virial.simulations.VirialAlkaneMix_Kong
VirialAlkaneMix_Kong.VirialAlkaneMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
VirialAlkaneSKS - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the SKS force field.
VirialAlkaneSKS() - Constructor for class etomica.virial.simulations.VirialAlkaneSKS
VirialAlkaneSKS.VirialSiepmannSpheresParam - Class in etomica.virial.simulations: Inner class for parameters
VirialAnthracene464 - Class in etomica.virial.simulations: Anthracene model , pure support for CO2/An mixture calculation 3 site model from Iwai, this is 464 model Mayer sampling to evaluate cluster integrals
VirialAnthracene464() - Constructor for class etomica.virial.simulations.VirialAnthracene464
VirialAnthracene464.VirialAnthracene545Param - Class in etomica.virial.simulations: 6 Inner class for parameters
VirialAnthracene545 - Class in etomica.virial.simulations: Anthracene model , pure support for CO2/An mixture calculation 3 site model from Iwai this is 545 model Mayer sampling to evaluate cluster integrals
VirialAnthracene545() - Constructor for class etomica.virial.simulations.VirialAnthracene545
VirialAnthracene545.VirialAnthracene545Param - Class in etomica.virial.simulations: 6 Inner class for parameters
VirialAnthracene545Param() - Constructor for class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
VirialAnthracene545Param() - Constructor for class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
VirialAnthraceneTraPPE - Class in etomica.virial.simulations: calculate the virial coefficients of Anthracene at given temperature united atom TraPPE model, LJ no electrostatic, reference: TraPPE , Siepmann * Mayer sampling to evaluate cluster integrals
VirialAnthraceneTraPPE() - Constructor for class etomica.virial.simulations.VirialAnthraceneTraPPE
VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam - Class in etomica.virial.simulations: 6 Inner class for parameters
VirialAnthraceneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
VirialAssociatingFluid - Class in etomica.virial.simulations
VirialAssociatingFluid() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid
VirialAssociatingFluid.VirialAssociatingFluidParam - Class in etomica.virial.simulations
VirialAssociatingFluid4points - Class in etomica.virial.simulations
VirialAssociatingFluid4points() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid4points
VirialAssociatingFluid4points.VirialAssociatingFluidParam - Class in etomica.virial.simulations
VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
VirialB3C1HSDipole - Class in etomica.virial.simulations: B3,C1, dielectric constant hard sphere with dipole in the center three f bonds with mu_i * mu_j June 2014
VirialB3C1HSDipole() - Constructor for class etomica.virial.simulations.VirialB3C1HSDipole
VirialB3C1HSDipole.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialB3C2HSDipole - Class in etomica.virial.simulations: B3,C2, dielectric constant part two, test hard sphere with dipole in the center June 2014
VirialB3C2HSDipole() - Constructor for class etomica.virial.simulations.VirialB3C2HSDipole
VirialB3C2HSDipole.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCH4AlkaneEHMix - Class in etomica.virial.simulations: Mayer sampling simulation for CH4(rigid, TraPPE-EH)-alkanes(TraPPE-EH) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialCH4AlkaneEHMix() - Constructor for class etomica.virial.simulations.VirialCH4AlkaneEHMix
VirialCH4AlkaneEHMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
virialCluster(int, MayerFunction, MayerFunction, byte) - Static method in class etomica.virial.cluster.ClusterAssociation
virialCluster(int, MayerFunction, boolean, MayerFunction, boolean) - Static method in class etomica.virial.cluster.Standard
virialClusterMixture(int, MayerFunction[][], MayerFunction[][], int[]) - Static method in class etomica.virial.cluster.Standard
virialClusterPolarizable(int, MayerFunction, boolean, boolean) - Static method in class etomica.virial.cluster.Standard
virialClusterXS(int, MayerFunction, boolean, MayerFunction, boolean, int) - Static method in class etomica.virial.cluster.Standard
VirialCO2 - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2() - Constructor for class etomica.virial.simulations.VirialCO2
VirialCO2.VirialCO2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2AlkaneEHMix - Class in etomica.virial.simulations: Mayer sampling simulation for CO2(rigid, TraPPE)-alkanes(TraPPE-EH) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams and flex diagrams are calculated separately (Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialCO2AlkaneEHMix() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneEHMix
VirialCO2AlkaneEHMix.VirialMixParam - Class in etomica.virial.simulations
VirialCO2AlkaneUAMix - Class in etomica.virial.simulations: Mayer sampling simulation for CO2(rigid, TraPPE)-alkanes(TraPPE-UA) mixture cross virial coefficients eovererr can be used Using VirialDiagramMix2 to generate diagrams see "VirialCO2AlkaneUARigid" B11 code(use rigid mix diagram) rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=0])
VirialCO2AlkaneUAMix() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneUAMix
VirialCO2AlkaneUAMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2anthracene464 - Class in etomica.virial.simulations: virial coefficients calculation mixture of CO2 and anthracene the code is modified from VirialCO2anthrancene545 Mayer sampling to evaluate cluster integrals CO2 is modeled as single site, anthracene is model as three site model (464) this is from Iwai et al, Monte carlo simulation of solubilities of Na, PH and An supercritical, Fluid Phase Equilibria 1998
VirialCO2anthracene464() - Constructor for class etomica.virial.simulations.VirialCO2anthracene464
VirialCO2anthracene464.VirialCO2anthracene545Param - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2anthracene545 - Class in etomica.virial.simulations: virial coefficients calculation mixture of CO2 and anthracene the code is modified from virialco2SKSmix Mayer sampling to evaluate cluster integrals CO2 is modeled as single site, anthracene is model as three site model this is from Iwai et al, Monte carlo simulation of solubilities of Na, PH and An supercritical, Fluid Phase Equilibria 1998 they modeled using 464 model or 545 model, this is 545 model
VirialCO2anthracene545() - Constructor for class etomica.virial.simulations.VirialCO2anthracene545
VirialCO2anthracene545.VirialCO2anthracene545Param - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2anthracene545Param() - Constructor for class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
VirialCO2anthracene545Param() - Constructor for class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
VirialCO2AnthraceneTraPPE - Class in etomica.virial.simulations: TraPPE mixture of CO2 and Anthracene the code is modified from CO2/naphthalene TraPPE LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2AnthraceneTraPPE() - Constructor for class etomica.virial.simulations.VirialCO2AnthraceneTraPPE
VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2AnthraceneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
VirialCO2CH4Mix - Class in etomica.virial.simulations: Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-EH) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams only since both of the components are rigid
VirialCO2CH4Mix() - Constructor for class etomica.virial.simulations.VirialCO2CH4Mix
VirialCO2CH4Mix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2CH4UAMix - Class in etomica.virial.simulations: Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-UA, single LJ site) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams both of the components are rigid
VirialCO2CH4UAMix() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMix
VirialCO2CH4UAMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2CH4UAMixWheatley - Class in etomica.virial.simulations: Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-UA, single LJ site) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams both of the components are rigid Implement Wheatley method
VirialCO2CH4UAMixWheatley() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMixWheatley
VirialCO2CH4UAMixWheatley.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2H2OGCPM - Class in etomica.virial.simulations: Computes CO2-H2O mixture virial coefficients using ab-initio potentials for both components.
VirialCO2H2OGCPM() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPM
VirialCO2H2OGCPM.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2H2OGCPMX - Class in etomica.virial.simulations: Computes CO2-H2O mixture virial coefficients using ab-initio potentials for both components.
VirialCO2H2OGCPMX() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPMX
VirialCO2H2OGCPMX.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2H2OSC - Class in etomica.virial.simulations: Computes CO2-H2O mixture virial coefficients using ab-initio potentials for both components.
VirialCO2H2OSC() - Constructor for class etomica.virial.simulations.VirialCO2H2OSC
VirialCO2H2OSC.VirialCO2SCParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2LJQ - Class in etomica.virial.simulations: single site LJ +QQ CO2 model , pure Mayer sampling to evaluate cluster integrals with overlap sampling From Albo model
VirialCO2LJQ() - Constructor for class etomica.virial.simulations.VirialCO2LJQ
VirialCO2LJQ.VirialCO2LJQParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2LJQParam() - Constructor for class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
VirialCO2N2Mix - Class in etomica.virial.simulations: Mayer sampling simulation for CO2(rigid, TraPPE)-N2(rigid, TraPPE) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams only since both of the components are rigid
VirialCO2N2Mix() - Constructor for class etomica.virial.simulations.VirialCO2N2Mix
VirialCO2N2Mix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2NaphthaleneLJQ - Class in etomica.virial.simulations: single site for CO2 and single site for naphthalene mixture of CO2 and Naphthalene the code is modified from virialco2SKSmix and virialCO2NaphthaleneTraPPE LJ simulation using Mayer sampling to evaluate cluster integrals parameters are from albo et al
VirialCO2NaphthaleneLJQ() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneLJQ
VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2NaphthaleneLJQParam() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
VirialCO2NaphthaleneTraPPE - Class in etomica.virial.simulations: TraPPE mixture of CO2 and Naphthalene the code is modified from virialco2SKSmix LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2NaphthaleneTraPPE() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE
VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2Param() - Constructor for class etomica.virial.simulations.VirialCO2.VirialCO2Param
VirialCO2Param() - Constructor for class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
VirialCO2PI - Class in etomica.virial.simulations: Mayer sampling simulation for path-integral virial coefficients of CO2.
VirialCO2PI() - Constructor for class etomica.virial.simulations.VirialCO2PI
VirialCO2PI.VirialH2PIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2SCParam() - Constructor for class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
VirialCO2SKSMix - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialCO2SKSMix() - Constructor for class etomica.virial.simulations.VirialCO2SKSMix
VirialCO2SKSMix.VirialCO2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2TraPPE - Class in etomica.virial.simulations: TraPPE CO2 model , pure LJ + electrostatic Mayer sampling to evaluate cluster integrals
VirialCO2TraPPE() - Constructor for class etomica.virial.simulations.VirialCO2TraPPE
VirialCO2TraPPE.VirialCO2TraPPEParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCO2TraPPEParam() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
VirialCO2TraPPEParam() - Constructor for class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
VirialCPSHeliumNonAdditive - Class in etomica.virial.simulations
VirialCPSHeliumNonAdditive() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditive
VirialCPSHeliumNonAdditive.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCPSHeliumNonAdditiveClassical - Class in etomica.virial.simulations
VirialCPSHeliumNonAdditiveClassical(ISpace) - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
VirialCPSHeliumNonAdditiveClassical.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialCPSHeliumNonAdditiveClassical_Correction - Class in etomica.virial.simulations
VirialCPSHeliumNonAdditiveClassical_Correction(ISpace) - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
virialData - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
VirialDiagrams - Class in etomica.virial.cluster
VirialDiagrams(int, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams
VirialDiagrams(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams
VirialDiagrams.ArticulatedAt0 - Class in etomica.virial.cluster
VirialDiagrams.ComparatorNumFieldNodesExchange - Class in etomica.virial.cluster
VirialDiagramsMix - Class in etomica.virial.cluster
VirialDiagramsMix(int, boolean[], boolean[]) - Constructor for class etomica.virial.cluster.VirialDiagramsMix
VirialDiagramsMix(int, boolean[], boolean[], boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsMix
VirialDiagramsMix2 - Class in etomica.virial.cluster
VirialDiagramsMix2(int, boolean[]) - Constructor for class etomica.virial.cluster.VirialDiagramsMix2
VirialDiagramsMix2(int, boolean[], boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsMix2
VirialDiagramsMix2.MaxIsomorphCriteriaMixture - Class in etomica.virial.cluster
VirialDiagramsPT - Class in etomica.virial.cluster
VirialDiagramsPT(int, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT
VirialDiagramsPT(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT
VirialDiagramsPT.ArticulatedAt0 - Class in etomica.virial.cluster
VirialDiagramsPT.ComparatorNumFieldNodesExchange - Class in etomica.virial.cluster
VirialDiagramsPT.DiscardCriteria - Class in etomica.virial.cluster
VirialEmulNonAdditive - Class in etomica.virial.simulations
VirialEmulNonAdditive() - Constructor for class etomica.virial.simulations.VirialEmulNonAdditive
VirialEmulNonAdditive.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialExternalFieldConfinedOverlap - Class in etomica.virial.simulations: External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldConfinedOverlap() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
VirialExternalFieldConfinedOverlap.VirialExternalFieldParam - Class in etomica.virial.simulations: Inner class for parameters
VirialExternalFieldConfinedOverlapRho - Class in etomica.virial.simulations: External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldConfinedOverlapRho() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam - Class in etomica.virial.simulations: Inner class for parameters
VirialExternalFieldConfinedOverlapSW - Class in etomica.virial.simulations: External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldConfinedOverlapSW() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam - Class in etomica.virial.simulations: Inner class for parameters
VirialExternalFieldOverlapRho - Class in etomica.virial.simulations: External Field simulation using Overlap2 sampling to evaluate cluster integrals
VirialExternalFieldOverlapRho() - Constructor for class etomica.virial.simulations.VirialExternalFieldOverlapRho
VirialExternalFieldOverlapRho.VirialExternalFieldParam - Class in etomica.virial.simulations: Inner class for parameters
VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
VirialGCPM - Class in etomica.virial.simulations
VirialGCPM() - Constructor for class etomica.virial.simulations.VirialGCPM
VirialGCPM.VirialGCPMParam - Class in etomica.virial.simulations: Inner class for parameters
VirialGCPMGraphic - Class in etomica.virial.simulations
VirialGCPMGraphic() - Constructor for class etomica.virial.simulations.VirialGCPMGraphic
VirialGCPMParam() - Constructor for class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
VirialH2O - Class in etomica.virial.simulations
VirialH2O() - Constructor for class etomica.virial.simulations.VirialH2O
VirialH2O.VirialH2OParam - Class in etomica.virial.simulations: Inner class for parameters
VirialH2OParam() - Constructor for class etomica.virial.simulations.VirialH2O.VirialH2OParam
VirialH2PI - Class in etomica.virial.simulations: Mayer sampling simulation
VirialH2PI() - Constructor for class etomica.virial.simulations.VirialH2PI
VirialH2PI.VirialH2PIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialH2PIBoltzmann - Class in etomica.virial.simulations
VirialH2PIBoltzmann() - Constructor for class etomica.virial.simulations.VirialH2PIBoltzmann
VirialH2PIBoltzmann.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialH2PIParam() - Constructor for class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
VirialH2PIParam() - Constructor for class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
VirialH2PISimple - Class in etomica.virial.simulations
VirialH2PISimple() - Constructor for class etomica.virial.simulations.VirialH2PISimple
VirialH2PISimple.VirialH2PISimpleParam - Class in etomica.virial.simulations: Inner class for parameters
VirialH2PISimpleParam() - Constructor for class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
VirialH2PIXC - Class in etomica.virial.simulations
VirialH2PIXC() - Constructor for class etomica.virial.simulations.VirialH2PIXC
VirialH2PIXC.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialH2PYCorrection - Class in etomica.virial.simulations: Computes corrections to Percus-Yevick approximations of B4 and B5 for a hydrogen pair potential.
VirialH2PYCorrection() - Constructor for class etomica.virial.simulations.VirialH2PYCorrection
VirialH2PYCorrection.VirialH2PYCParam - Class in etomica.virial.simulations: Inner class for parameters
VirialH2PYCParam() - Constructor for class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
VirialHardAssociationCone - Class in etomica.virial.simulations: Virial coefficients with single attraction site AssociationCone Potential using Mayer Sampling
VirialHardAssociationCone() - Constructor for class etomica.virial.simulations.VirialHardAssociationCone
VirialHardAssociationCone.VirialLJParam - Class in etomica.virial.simulations
VirialHardAssociationConeDoubleSites - Class in etomica.virial.simulations: Virial coefficients with double attraction site AssociationCone Potential using Mayer Sampling
VirialHardAssociationConeDoubleSites() - Constructor for class etomica.virial.simulations.VirialHardAssociationConeDoubleSites
VirialHardAssociationConeDoubleSites.VirialLJParam - Class in etomica.virial.simulations
VirialHeNonAdditive - Class in etomica.virial.simulations
VirialHeNonAdditive() - Constructor for class etomica.virial.simulations.VirialHeNonAdditive
VirialHeNonAdditive.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHeNonAdditiveWheatley - Class in etomica.virial.simulations: Adapted by Andrew from VirialHeNonAdditive Computes only the nonadditive component of either the third, fourth, or fifth virial coefficient for the ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz (JCP 131 064105 2009).
VirialHeNonAdditiveWheatley() - Constructor for class etomica.virial.simulations.VirialHeNonAdditiveWheatley
VirialHeNonAdditiveWheatley.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePCKLJS - Class in etomica.virial.simulations: Computes additive virial coefficients using the pair potential for He of Przybytek et al.
VirialHePCKLJS() - Constructor for class etomica.virial.simulations.VirialHePCKLJS
VirialHePCKLJS.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePCKLJSCHNCCorrection - Class in etomica.virial.simulations: Computes corrections to hypernetted-chain approximations of B4 and B5 for a helium pair potential.
VirialHePCKLJSCHNCCorrection() - Constructor for class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection
VirialHePCKLJSCHNCCorrection.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePCKLJSPYCorrection - Class in etomica.virial.simulations: Computes corrections to Percus-Yevick approximations of B4 and B5 for a helium pair potential.
VirialHePCKLJSPYCorrection() - Constructor for class etomica.virial.simulations.VirialHePCKLJSPYCorrection
VirialHePCKLJSPYCorrection.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePCKLJSTempDeriv - Class in etomica.virial.simulations: Computes first or second temperatures (see firstDerivative variable) of additive virial coefficients using the ab initio pair potential for helium from Przybytek et al.
VirialHePCKLJSTempDeriv() - Constructor for class etomica.virial.simulations.VirialHePCKLJSTempDeriv
VirialHePCKLJSTempDeriv.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePI - Class in etomica.virial.simulations: Mayer sampling simulation
VirialHePI() - Constructor for class etomica.virial.simulations.VirialHePI
VirialHePI.FlexApproach - Enum in etomica.virial.simulations
VirialHePI.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePI_PotentialCorrection - Class in etomica.virial.simulations: Mayer sampling simulation
VirialHePI_PotentialCorrection() - Constructor for class etomica.virial.simulations.VirialHePI_PotentialCorrection
VirialHePI_PotentialCorrection.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePIGraphic - Class in etomica.virial.simulations: Mayer sampling simulation
VirialHePIGraphic() - Constructor for class etomica.virial.simulations.VirialHePIGraphic
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePI.VirialHePIParam
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
VirialHePIXC - Class in etomica.virial.simulations: Mayer sampling simulation for alkanes using the TraPPE force field.
VirialHePIXC() - Constructor for class etomica.virial.simulations.VirialHePIXC
VirialHePIXC.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePIXCEven - Class in etomica.virial.simulations: MSMC calculation for the "even" exchange component of helium-4 virial coefficients.
VirialHePIXCEven() - Constructor for class etomica.virial.simulations.VirialHePIXCEven
VirialHePIXCEven.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePIXCOdd - Class in etomica.virial.simulations: MSMC calculation for pieces of the "odd" exchange component of helium-4 virial coefficients.
VirialHePIXCOdd() - Constructor for class etomica.virial.simulations.VirialHePIXCOdd
VirialHePIXCOdd.VirialHePIParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePYCorrection - Class in etomica.virial.simulations: Computes corrections to Percus-Yevick approximations of B4 and B5 for a helium pair potential.
VirialHePYCorrection() - Constructor for class etomica.virial.simulations.VirialHePYCorrection
VirialHePYCorrection.VirialHePYCParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHePYCParam() - Constructor for class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
VirialHePYCParam() - Constructor for class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
VirialHeSC - Class in etomica.virial.simulations: Computes virial coefficients for a helium pair potential.
VirialHeSC() - Constructor for class etomica.virial.simulations.VirialHeSC
VirialHeSC.VirialHePYCParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHS - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialHS() - Constructor for class etomica.virial.simulations.VirialHS
VirialHS.VirialHSParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHSBinMultiThreaded - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialHSBinMultiThreaded() - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded
VirialHSBinMultiThreaded.DooDad - Class in etomica.virial.simulations
VirialHSBinMultiThreaded.SimulationWorker - Class in etomica.virial.simulations
VirialHSBinMultiThreaded.VirialHSBinParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHSBinParam() - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
VirialHSBinParam() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
VirialHSOrC - Class in etomica.virial.simulations: Overlap sampling simulation to compute c(r) for HS
VirialHSOrC() - Constructor for class etomica.virial.simulations.VirialHSOrC
VirialHSOrC.PotentialChoice - Enum in etomica.virial.simulations
VirialHSOrC.VirialLJrParam - Class in etomica.virial.simulations: Inner class for parameters
VirialHSParam() - Constructor for class etomica.virial.simulations.VirialHS.VirialHSParam
VirialHSParam() - Constructor for class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
VirialHSParam() - Constructor for class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
VirialHSParam() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
VirialHSParam() - Constructor for class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
VirialLJ - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJ() - Constructor for class etomica.virial.simulations.VirialLJ
VirialLJ.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJBridge - Class in etomica.virial.simulations: MSMC computations (via overlap sampling) of the bridge diagram(s) within the f-bond-only formulation.
VirialLJBridge() - Constructor for class etomica.virial.simulations.VirialLJBridge
VirialLJBridge.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJCHNCCorrection - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate corrections to the HNC(c) approximations to B4 and B5
VirialLJCHNCCorrection() - Constructor for class etomica.virial.simulations.VirialLJCHNCCorrection
VirialLJCHNCCorrection.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJMultiOverlap - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJMultiOverlap() - Constructor for class etomica.virial.simulations.VirialLJMultiOverlap
VirialLJMultiOverlap.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJOrC - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJOrC() - Constructor for class etomica.virial.simulations.VirialLJOrC
VirialLJOrC.PotentialChoice - Enum in etomica.virial.simulations
VirialLJOrC.VirialLJrParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJOrICPYC - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJOrICPYC() - Constructor for class etomica.virial.simulations.VirialLJOrICPYC
VirialLJOrICPYC.VirialLJrParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJParam() - Constructor for class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJ.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJBridge.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJSeries.VirialLJParam
VirialLJPYCorrection - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to evaluate corrections to the PY(c) approximations to B4 and B5
VirialLJPYCorrection() - Constructor for class etomica.virial.simulations.VirialLJPYCorrection
VirialLJPYCorrection.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialLJQB2 - Class in etomica.modules.vle: LJ simulation using Mayer sampling to evaluate cluster integrals
VirialLJQB2() - Constructor for class etomica.modules.vle.VirialLJQB2
VirialLJrParam() - Constructor for class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
VirialLJrParam() - Constructor for class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
VirialLJrParam() - Constructor for class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
VirialLJSeries - Class in etomica.virial.simulations: LJ simulation using Mayer sampling to integrals that show up in series expansion.
VirialLJSeries() - Constructor for class etomica.virial.simulations.VirialLJSeries
VirialLJSeries.VirialLJParam - Class in etomica.virial.simulations: Inner class for parameters
VirialMethaneEH - Class in etomica.virial.simulations: TraPPE-EH methane, CH4 Mayer sampling to evaluate cluster integrals
VirialMethaneEH() - Constructor for class etomica.virial.simulations.VirialMethaneEH
VirialMethaneEH.VirialMethaneParam - Class in etomica.virial.simulations: Inner class for parameters
VirialMethaneParam() - Constructor for class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
VirialMixParam() - Constructor for class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
VirialN2 - Class in etomica.virial.simulations
VirialN2() - Constructor for class etomica.virial.simulations.VirialN2
VirialN2.VirialN2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialN2AlkaneEHMix - Class in etomica.virial.simulations: Mayer sampling simulation for N2(rigid, TraPPE)-alkanes(TraPPE-EH) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialN2AlkaneEHMix() - Constructor for class etomica.virial.simulations.VirialN2AlkaneEHMix
VirialN2AlkaneEHMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialN2AlkaneUAMix - Class in etomica.virial.simulations: Mayer sampling simulation for N2(rigid, TraPPE)-alkanes(TraPPE-UA) mixture Martin and Siepmann, JPC(B) 102, 2569-2577 (1998) eovererr can be used cross virial coefficients Using VirialDiagramMix2 to generate diagrams see "VirialN2AlkaneUARigid" B11 code(use rigid mix diagram) rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
VirialN2AlkaneUAMix() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUAMix
VirialN2AlkaneUAMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialN2AlkaneUARigid - Class in etomica.virial.simulations: cross virial coefficients of mixture of N2 and alkanes(TraPPE-UA) no flexible diagrams, just rigid diagrams just for B11, see "VirialN2AlkaneMix" for flexible corrections N2:use CO2EMP, C<==> "A", O<==>"N"
VirialN2AlkaneUARigid() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUARigid
VirialN2AlkaneUARigid.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialN2CH4Mix - Class in etomica.virial.simulations: Mayer sampling simulation for N2(rigid, TraPPE)-CH4(TraPPE-EH) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams
VirialN2CH4Mix() - Constructor for class etomica.virial.simulations.VirialN2CH4Mix
VirialN2CH4Mix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialN2CH4UAMix - Class in etomica.virial.simulations: Mayer sampling simulation for N2(rigid, TraPPE)-CH4(rigid, TraPPE-UA) mixture cross virial coefficients Using VirialDiagramMix2 to generate diagrams rigid diagrams only since both of the components are rigid
VirialN2CH4UAMix() - Constructor for class etomica.virial.simulations.VirialN2CH4UAMix
VirialN2CH4UAMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialN2Param() - Constructor for class etomica.virial.simulations.VirialN2.VirialN2Param
VirialN2Param() - Constructor for class etomica.virial.simulations.VirialN2PI.VirialN2Param
VirialN2Param() - Constructor for class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
VirialN2PI - Class in etomica.virial.simulations
VirialN2PI() - Constructor for class etomica.virial.simulations.VirialN2PI
VirialN2PI.VirialN2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialN2TraPPE - Class in etomica.virial.simulations: TraPPE N2 model Potoff and Siepmann.
VirialN2TraPPE() - Constructor for class etomica.virial.simulations.VirialN2TraPPE
VirialN2TraPPE.VirialN2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialNaphthaleneTraPPE - Class in etomica.virial.simulations: TraPPE Naphthalene model , pure LJ no electrostatic Mayer sampling to evaluate cluster integrals reference: TraPPE 4, Siepmann
VirialNaphthaleneTraPPE() - Constructor for class etomica.virial.simulations.VirialNaphthaleneTraPPE
VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam - Class in etomica.virial.simulations: 6 Inner class for parameters
VirialNaphthaleneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
virialNonAdditiveTrimerEnergy(int, MayerFunction, Potential, boolean, boolean) - Static method in class etomica.virial.cluster.Standard
VirialO2 - Class in etomica.virial.simulations
VirialO2() - Constructor for class etomica.virial.simulations.VirialO2
VirialO2.VirialO2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialO2Param() - Constructor for class etomica.virial.simulations.VirialO2.VirialO2Param
VirialO2Param() - Constructor for class etomica.virial.simulations.VirialO2PI.VirialO2Param
VirialO2PI - Class in etomica.virial.simulations
VirialO2PI() - Constructor for class etomica.virial.simulations.VirialO2PI
VirialO2PI.VirialO2Param - Class in etomica.virial.simulations: Inner class for parameters
VirialOptimizer - Class in etomica.util.numerical: Class to determine B9 value that best fit the simulation results after Pade Approximation [K/L]
VirialOptimizer(String, String) - Constructor for class etomica.util.numerical.VirialOptimizer
VirialOptimizer.VirialParam - Class in etomica.util.numerical
VirialParam() - Constructor for class etomica.util.numerical.B9Optimizer.VirialParam
VirialParam() - Constructor for class etomica.util.numerical.PadeApproximation.VirialParam
VirialParam() - Constructor for class etomica.util.numerical.VirialOptimizer.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.ReeHooverMC.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialAceticAcid.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJS.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
VirialParam() - Constructor for class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
VirialPh3site464Param() - Constructor for class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
VirialPh3site545Param() - Constructor for class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
VirialPh464 - Class in etomica.virial.simulations: Phenanthrene model , pure support for CO2/phenanthrene mixture calculation 3 site model from Iwai this is 464 model Mayer sampling to evaluate cluster integrals
VirialPh464() - Constructor for class etomica.virial.simulations.VirialPh464
VirialPh464.VirialPh3site464Param - Class in etomica.virial.simulations: 6 Inner class for parameters
VirialPh545 - Class in etomica.virial.simulations: Phenanthrene model , pure support for CO2/phenanthrene mixture calculation 3 site model from Iwai this is 545 model Mayer sampling to evaluate cluster integrals
VirialPh545() - Constructor for class etomica.virial.simulations.VirialPh545
VirialPh545.VirialPh3site545Param - Class in etomica.virial.simulations: 6 Inner class for parameters
VirialPhenanthreneTraPPE - Class in etomica.virial.simulations: TraPPE phenanthrene model , pure LJ no electrostatic Mayer sampling to evaluate cluster integrals reference: TraPPE 4, Siepmann
VirialPhenanthreneTraPPE() - Constructor for class etomica.virial.simulations.VirialPhenanthreneTraPPE
VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam - Class in etomica.virial.simulations: Inner class for parameters
VirialPhenanthreneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
VirialPolyhedra - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialPolyhedra() - Constructor for class etomica.virial.simulations.VirialPolyhedra
VirialPolyhedra.DataProcessorR2 - Class in etomica.virial.simulations
VirialPolyhedra.VirialHSParam - Class in etomica.virial.simulations: Inner class for parameters
VirialPolyhedra2 - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialPolyhedra2() - Constructor for class etomica.virial.simulations.VirialPolyhedra2
VirialPolyhedra2.DataProcessorR2 - Class in etomica.virial.simulations
VirialPolyhedra2.VirialHSParam - Class in etomica.virial.simulations: Inner class for parameters
virialProfile - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
virialProfileWork - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
VirialRowleyAlcohol - Class in etomica.virial.simulations: Mayer-sampling MC simulation for methanol or ethanol using the potentials published in: R.L.
VirialRowleyAlcohol() - Constructor for class etomica.virial.simulations.VirialRowleyAlcohol
VirialRowleyAlcohol.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
virialSeriesCluster(int, MayerFunction[], int[]) - Static method in class etomica.virial.cluster.Standard
VirialSF6LJAlkaneUAMix - Class in etomica.virial.simulations: Mayer sampling simulation for SF6(rigid, LJ sphere)-alkanes(TraPPE-UA) mixture cross virial coefficients eovererr can be used Using VirialDiagramMix2 to generate diagrams rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=0])
VirialSF6LJAlkaneUAMix() - Constructor for class etomica.virial.simulations.VirialSF6LJAlkaneUAMix
VirialSF6LJAlkaneUAMix.VirialMixParam - Class in etomica.virial.simulations: Inner class for parameters
VirialSF6Param() - Constructor for class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
VirialSQWBinMultiRecalcW - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialSQWBinMultiRecalcW() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiRecalcW
VirialSQWBinMultiRecalcW.VirialHSParam - Class in etomica.virial.simulations: Inner class for parameters
VirialSQWBinMultiThreaded - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialSQWBinMultiThreaded() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded
VirialSQWBinMultiThreaded.SimulationWorker - Class in etomica.virial.simulations
VirialSQWBinMultiThreaded.VirialHSBinParam - Class in etomica.virial.simulations: Inner class for parameters
VirialSQWRecalcSmallMem - Class in etomica.virial.simulations: Calculation for virial coefficients of hard spheres
VirialSQWRecalcSmallMem() - Constructor for class etomica.virial.simulations.VirialSQWRecalcSmallMem
VirialSQWRecalcSmallMem.VirialHSParam - Class in etomica.virial.simulations: Inner class for parameters
virialSum - Variable in class etomica.data.meter.MeterPressureHard
virialSum - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
virialSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
virialSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
virialSumCO - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
virialSumCO2 - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
virialSumIG - Variable in class etomica.modules.mu.DataSourceWallPressureMu
virialSumO2 - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
virialSumSQW - Variable in class etomica.modules.mu.DataSourceWallPressureMu
VirialSW - Class in etomica.virial.simulations: SW simulation using Mayer sampling to evaluate cluster integrals
VirialSW() - Constructor for class etomica.virial.simulations.VirialSW
VirialSW.VirialSWParam - Class in etomica.virial.simulations: Inner class for parameters
VirialSWParam() - Constructor for class etomica.virial.simulations.VirialSW.VirialSWParam
VirialSwsPT - Class in etomica.virial.simulations
VirialSwsPT() - Constructor for class etomica.virial.simulations.VirialSwsPT
VirialSwsPT.VirialSiepmannSpheresParam - Class in etomica.virial.simulations: Inner class for parameters
VirialSWWE - Class in etomica.virial.simulations
VirialSWWE() - Constructor for class etomica.virial.simulations.VirialSWWE
VirialSWWE.VirialSWWEParam - Class in etomica.virial.simulations: Inner class for parameters
VirialSWWEParam() - Constructor for class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
VirialTraPPEAlcohol - Class in etomica.virial.simulations: Mayer-sampling MC simulation for methanol or ethanol using the TraPPE model: http://www.chem.umn.edu/groups/siepmann/trappe/intro.php Set species, model (with or without point charges), virial-coefficent type (B2, B3, etc.), and temperature in VirialParam() method at bottom of file.
VirialTraPPEAlcohol() - Constructor for class etomica.virial.simulations.VirialTraPPEAlcohol
VirialTraPPEAlcohol.VirialParam - Class in etomica.virial.simulations: Inner class for parameters
VirialWaterOverlap - Class in etomica.virial.simulations: Generic simulation using Mayer sampling to evaluate cluster integrals
VirialWaterOverlap() - Constructor for class etomica.virial.simulations.VirialWaterOverlap
viscosity() - Method in class etomica.units.systems.CGS
viscosity() - Method in class etomica.units.systems.LJ
viscosity() - Method in class etomica.units.systems.MKS
viscosity() - Method in class etomica.units.systems.UnitSystem.Sim
viscosity() - Method in class etomica.units.systems.UnitSystem
Viscosity - Class in etomica.units: Dimension for all units of viscosity, Mass/(Length-Time)
visit(Edge) - Method in interface etomica.graph.model.EdgeVisitor
visit(Node) - Method in interface etomica.graph.model.NodeVisitor
visit(byte) - Method in class etomica.graph.traversal.AbstractTraversal
visit(byte, byte) - Method in class etomica.graph.traversal.BCVisitor
visit(byte, byte) - Method in class etomica.graph.traversal.CVisitor
visit(byte, byte) - Method in interface etomica.graph.traversal.TraversalVisitor
visited - Variable in class etomica.graph.traversal.Biconnected
visitEdges(EdgeVisitor) - Method in interface etomica.graph.model.Graph
visitEdges(EdgeVisitor) - Method in class etomica.graph.model.impl.GraphImpl
visitNodes(NodeVisitor) - Method in interface etomica.graph.model.Graph
visitNodes(NodeVisitor) - Method in class etomica.graph.model.impl.GraphImpl
visualrange - Static variable in class org.jmol.script.Token
VLE - Class in etomica.modules.vle
VLE(VLESim, ISpace) - Constructor for class etomica.modules.vle.VLE
VLE.Applet - Class in etomica.modules.vle
VLESim - Class in etomica.modules.vle
VLESim() - Constructor for class etomica.modules.vle.VLESim
vmax - Variable in class etomica.modules.clustergenerator.Plot
vmin - Variable in class etomica.modules.clustergenerator.Plot
vN2Angles(double, double, double, double) - Method in class etomica.potential.P2NitrogenHellmann
vNew - Variable in class etomica.integrator.mcmove.MCMoveVolume
vNew - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
Vnlll - Variable in class etomica.potential.P2HydrogenPatkowski
Vnlll - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
vOH - Variable in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
vOH - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
vol - Variable in class etomica.mappedvirial.MappedUpotential
vol - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
vol - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
vOld - Variable in class etomica.modules.adsorption.P1Wall
vOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
Volt - Class in etomica.units: The Volt unit of electric potential.
volume() - Method in interface etomica.api.IBoundary
volume() - Method in class etomica.modules.pistoncylinder.BoundaryPistonCylinder
volume - Variable in class etomica.normalmode.DataSourceAvgPressure2
volume - Variable in class etomica.normalmode.DataSourceMuRoot
volume - Variable in class etomica.normalmode.DataSourceMuRoot1
volume - Variable in class etomica.normalmode.DataSourceMuRootPMatch
volume - Variable in class etomica.normalmode.DataSourcePMu
volume - Variable in class etomica.normalmode.MeterSolidProps
volume - Variable in class etomica.normalmode.MeterSolidPropsLJ
volume - Variable in class etomica.normalmode.PotentialCalculationEFSSP
volume - Variable in class etomica.normalmode.PotentialCalculationLJSP
volume - Variable in class etomica.potential.EwaldSummation
volume - Variable in class etomica.potential.EwaldSumMolecules
volume() - Method in class etomica.space.Boundary
volume() - Method in class etomica.space.BoundaryDeformablePeriodic
volume() - Method in class etomica.space.BoundaryRectangular: Returns the "volume" of the rectangular region defined by this Boundary.
volume() - Method in class etomica.units.systems.CGS
volume() - Method in class etomica.units.systems.LJ
volume() - Method in class etomica.units.systems.MKS
volume() - Method in class etomica.units.systems.UnitSystem.Sim
volume() - Method in class etomica.units.systems.UnitSystem
Volume - Class in etomica.units: Dimension for all volume units.
volume - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
volume - Static variable in class org.jmol.script.Token
VolumeBias(double, int) - Constructor for class etomica.liquidLJ.LjMd3D.VolumeBias
volumeChanges - Variable in class etomica.modules.ensembles.LJMCGraphic
volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
vp(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
vp(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
vp(double, double) - Method in interface etomica.mappedvirial.PotentialCalculationMappedVirialV.VFunc
vScale - Variable in class etomica.integrator.mcmove.MCMoveVolume
vScale - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
vSource - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
vSums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff

W

w - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
w - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
w - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
w - Variable in class etomica.meam.EFSTungsten
w - Variable in class etomica.modules.materialfracture.P1Tension
W - Variable in class etomica.modules.rheology.IntegratorPolymer
w - Variable in class etomica.potential.P2SpheroPolyhedron
w - Variable in class etomica.potential.P3HydrogenManzhos
w - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
w - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
w - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
w - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
w - Variable in class org.jmol.util.Tuple4f: The w coordinate.
W0 - Variable in class etomica.potential.P2SpheroPolyhedron
W1 - Variable in class etomica.potential.P2SpheroPolyhedron
W2 - Variable in class etomica.potential.P2SpheroPolyhedron
w3j - Variable in class etomica.potential.P2HydrogenPatkowski
w3j - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
wA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
wA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
waitformoveto - Static variable in class org.jmol.script.Token
waitObject - Variable in class etomica.action.activity.Controller
WaitObject() - Constructor for class etomica.action.activity.Controller.WaitObject
walk(Graph, List<Byte>, byte, byte, byte) - Method in class etomica.graph.property.FFTDecomposition
walk(Graph, List<Byte>, byte, byte, byte) - Method in class etomica.graph.property.IsFFT
walkDimer() - Method in class etomica.dimer.IntegratorDimerMin: Moves the half-dimer stepLength*N towards the energy minimum.
wallButton - Variable in class etomica.modules.sam.SamGraphic
wallDim - Variable in class etomica.modules.dcvgcmd.P1WCAWall
wallDim - Variable in class etomica.modules.sam.P1WCAWall
walldistance - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
walldistance - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
walldistance - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
wallForce - Variable in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
wallForce - Variable in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
wallForceSum - Variable in class etomica.modules.sam.PotentialCalculationForceSumWall
WallPlane - Class in etomica.modules.sam: Wrap a P1WCAWall and make it look like a Plane.
WallPlane(ISpace, P1WCAWall) - Constructor for class etomica.modules.sam.WallPlane
wallPosition - Variable in class etomica.modules.sam.P1WCAWall
wallPotential - Variable in class etomica.modules.pistoncylinder.DataSourceWallPressure
wallPotential - Variable in class etomica.modules.pistoncylinder.PistonCylinder
wallPotential - Variable in class etomica.modules.sam.PotentialCalculationForceSumWall
wallPotential - Variable in class etomica.modules.sam.Sam
wallPotential - Variable in class etomica.modules.sam.WallPlane
WallRangeModifier(P1Wall, CriterionPositionWall) - Constructor for class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
wallSpecies - Variable in class etomica.interfacial.MeterWallPosition
warn(String) - Method in class org.jmol.util.DefaultLogger
warn(String) - Static method in class org.jmol.util.Logger: Writes a log at WARN level.
warn(String) - Method in interface org.jmol.util.LoggerInterface: Writes a log at WARN level.
warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
warnEx(String, Throwable) - Static method in class org.jmol.util.Logger: Writes a log at WARN level with detail on exception.
warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface: Writes a log at WARN level with detail on exception.
warningPrinted - Variable in class etomica.potential.PotentialCalculationPressureTensor
WaterBox - Class in etomica.rotation
WaterBox() - Constructor for class etomica.rotation.WaterBox
WaterBox.Applet - Class in etomica.rotation
WaterDroplet - Class in etomica.rotation
WaterDroplet() - Constructor for class etomica.rotation.WaterDroplet
WaterDroplet.Applet - Class in etomica.rotation
WaterDropletMatrix - Class in etomica.rotation
WaterDropletMatrix() - Constructor for class etomica.rotation.WaterDropletMatrix
WaterDropletMatrix.Applet - Class in etomica.rotation
WaterDropletRattle - Class in etomica.rotation
WaterDropletRattle() - Constructor for class etomica.rotation.WaterDropletRattle
WaterDropletRattle.Applet - Class in etomica.rotation
WaterDropletShake - Class in etomica.rotation
WaterDropletShake() - Constructor for class etomica.rotation.WaterDropletShake
WaterDropletShake.Applet - Class in etomica.rotation
WaterTrimer - Class in etomica.rotation
WaterTrimer() - Constructor for class etomica.rotation.WaterTrimer
WaterTrimer.Applet - Class in etomica.rotation
WaterTrimerRattle - Class in etomica.rotation
WaterTrimerRattle() - Constructor for class etomica.rotation.WaterTrimerRattle
WaterTrimerRattle.Applet - Class in etomica.rotation
WaterTrimerShake - Class in etomica.rotation
WaterTrimerShake() - Constructor for class etomica.rotation.WaterTrimerShake
WaterTrimerShake.Applet - Class in etomica.rotation
waveVec - Variable in class etomica.data.meter.MeterStructureFactor
waveVector - Variable in class etomica.normalmode.MeterHarmonicCoordinate
waveVectorAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
waveVectorCoefficients - Variable in class etomica.normalmode.CalcJacobian
waveVectorCoefficients - Variable in class etomica.normalmode.MeterHarmonicEnergy
waveVectorCoefficients - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
waveVectorFactory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
waveVectorFactory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
waveVectorFactory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
waveVectorFactory - Variable in class etomica.normalmode.NormalModes2D
waveVectorFactory - Variable in class etomica.normalmode.NormalModes3D
WaveVectorFactory - Interface in etomica.normalmode: Interface for a class the returns the appropriate wave vectors for a box and primitive
waveVectorFactory - Variable in class etomica.normalmode.WriteS
WaveVectorFactory1D - Class in etomica.normalmode: Wave vector factory that returns wave vectors for a 1D system.
WaveVectorFactory1D() - Constructor for class etomica.normalmode.WaveVectorFactory1D
WaveVectorFactory2D - Class in etomica.normalmode: Wave vector factory that returns wave vectors appropriate for a box with a single-atom basis.
WaveVectorFactory2D(Primitive, ISpace) - Constructor for class etomica.normalmode.WaveVectorFactory2D
WaveVectorFactoryFcc - Class in etomica.normalmode: WaveVectorFactory implementation that returns wave vectors appropriate for a cubic FCC lattice.
WaveVectorFactoryFcc(PrimitiveFcc, int) - Constructor for class etomica.normalmode.WaveVectorFactoryFcc
WaveVectorFactoryFromFile - Class in etomica.normalmode: Obtains wave vectors and coefficients from a file.
WaveVectorFactoryFromFile(String, int) - Constructor for class etomica.normalmode.WaveVectorFactoryFromFile
WaveVectorFactorySimple - Class in etomica.normalmode: Wave vector factory that returns wave vectors appropriate for a box with a single-atom basis.
WaveVectorFactorySimple(Primitive, ISpace) - Constructor for class etomica.normalmode.WaveVectorFactorySimple
WaveVectorFactorySuperBox - Class in etomica.normalmode
WaveVectorFactorySuperBox(Primitive, ISpace) - Constructor for class etomica.normalmode.WaveVectorFactorySuperBox
waveVectorMethod - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
waveVectorMethod - Variable in class etomica.normalmode.NormalModesMolecular
waveVectorNum - Variable in class etomica.normalmode.IntegratorHarmonic
waveVectorPostAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
waveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
waveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
waveVectors - Variable in class etomica.modules.sam.P1Sinusoidal
waveVectors - Variable in class etomica.normalmode.CalcJacobian
waveVectors - Variable in class etomica.normalmode.MeterHarmonicEnergy
waveVectors - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
waveVectors - Variable in class etomica.normalmode.NormalModesVariable
waveVectors - Variable in class etomica.normalmode.WaveVectorFactory1D
waveVectors - Variable in class etomica.normalmode.WaveVectorFactory2D
waveVectors - Variable in class etomica.normalmode.WaveVectorFactoryFcc
waveVectors - Variable in class etomica.normalmode.WaveVectorFactorySimple
wavevectorx - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
wavevectory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
wavevectorz - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
wB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
wB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
weight - Variable in class etomica.tmmc.IntegratorTMMC
weight - Variable in class etomica.virial.MeterVirialBDBin
weight - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
weight - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
weight - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
weightCluster - Variable in class etomica.virial.ClusterWeightAbs
weightNew - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
weightNew - Variable in class etomica.virial.MCMoveClusterRingRegrow
weightNew - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
weightNew - Variable in class etomica.virial.MCMoveClusterRingScale
weightOld - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
weightOld - Variable in class etomica.virial.MCMoveClusterRingRegrow
weightOld - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
weightOld - Variable in class etomica.virial.MCMoveClusterRingScale
weightSum - Variable in class etomica.util.HistogramReweightedData
well2 - Variable in class etomica.virial.MayerWell
wellConstant - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
wellConstant - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
wellConstant - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
wellDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBonding
wellDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
wellDiameter - Variable in class etomica.modules.catalysis.P2SquareWellSurface
wellDiameter - Variable in class etomica.modules.mu.P2SquareWellOneSide
wellDiameter - Variable in class etomica.potential.P2DoubleWell
wellDiameter - Variable in class etomica.potential.P2SquareWell
wellDiameter - Variable in class etomica.potential.P2SquareWellRobust
wellDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBonding
wellDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
wellDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellSurface
wellDiameterSquared - Variable in class etomica.modules.mu.P2SquareWellOneSide
wellDiameterSquared - Variable in class etomica.potential.P2DoubleWell
wellDiameterSquared - Variable in class etomica.potential.P2PenetrableSquareWell
wellDiameterSquared - Variable in class etomica.potential.P2SquareWell
wellDiameterSquared - Variable in class etomica.potential.P2SquareWellRobust
wellManager - Variable in class etomica.potential.P2SquareWellRobust
Wertheim2SiteAceticAcid - Class in etomica.association.AceticAcid: Wertheim coefficients calculation for acetic acid using IMPROVED OPLS united-atom model.
Wertheim2SiteAceticAcid() - Constructor for class etomica.association.AceticAcid.Wertheim2SiteAceticAcid
Wertheim2SiteAceticAcid.WertheimParam - Class in etomica.association.AceticAcid: Inner class for parameters
WertheimAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
WertheimDiagrams2SiteRho - Class in etomica.virial.cluster: Wertheim diagram generator for 2 site model
WertheimDiagrams2SiteRho(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams2SiteRho
WertheimDiagrams2SiteRho(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams2SiteRho
WertheimDiagrams3SiteRho - Class in etomica.virial.cluster: Wertheim diagram generator for GCPM water (3 site model)
WertheimDiagrams3SiteRho(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams3SiteRho
WertheimDiagrams3SiteRho(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams3SiteRho
WertheimGCPM3PtEBondDecomp - Class in etomica.association.GCPMWater: repulsive potential: energy of pair is greater than -3000cal/mol attractive potential: energy of pair is less than -3000cal/mol Wertheim's single attraction-site model of GCPM Three Site model e-bond in 3 body term is decomposed into eR and F
WertheimGCPM3PtEBondDecomp() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp
WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
WertheimGCPM3PtThreeSite - Class in etomica.association.GCPMWater: repulsive potential: energy of pair is greater than -association energy(cal/mol) attractive potential: energy of pair is less than -association energy(cal/mol) Wertheim's three attraction-site model of GCPM Three point diagram Three Site model
WertheimGCPM3PtThreeSite() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite
WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
WertheimGCPM4PtEBondDecomp - Class in etomica.association.GCPMWater: repulsive potential: energy of pair is greater than -2500cal/mol attractive potential: energy of pair is less than -2500cal/mol Wertheim's single attraction-site model of GCPM Three Site model e-bond in 4 body term is decomposed into eR and F final revision Aug 2011
WertheimGCPM4PtEBondDecomp() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp
WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam - Class in etomica.association.GCPMWater
WertheimGCPM4PtEBondDecompFinal - Class in etomica.association.GCPMWater: repulsive potential: energy of pair is greater than -3000cal/mol attractive potential: energy of pair is less than -3000cal/mol Wertheim's single attraction-site model of GCPM Three Site model e-bond in 4 body term is decomposed into eR and F Flipping is applied in 28E calculation final revision Aug 2011
WertheimGCPM4PtEBondDecompFinal() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal
WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
WertheimGCPM4PtThreeSite - Class in etomica.association.GCPMWater: repulsive potential: energy of pair is greater than -association E(cal/mol) attractive potential: energy of pair is less than -association E(cal/mol) Wertheim's three attraction-site model of GCPM 4th order diagram last revision Aug 2011
WertheimGCPM4PtThreeSite() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite
WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
WertheimGCPM4PtThreeSiteEDecompDirectSampling - Class in etomica.association.GCPMWater: repulsive potential: energy of pair is greater than -association E(cal/mol) attractive potential: energy of pair is less than -association E(cal/mol) Wertheim's three attraction-site model of GCPM Direct Sampling Non-additive 4th order diagram
WertheimGCPM4PtThreeSiteEDecompDirectSampling() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling
WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
WertheimParam() - Constructor for class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
WEST - Static variable in class etomica.util.Constants.CompassDirection
which - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
whichGraph - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
WHITE - Static variable in class org.jmol.util.Colix
widom2Plot - Variable in class etomica.modules.insertion.InsertionGraphic
widomHistPlot - Variable in class etomica.modules.insertion.InsertionGraphic
width - Variable in class etomica.graph.view.rasterizer.SVGConverter: Output image width.
WIDTH - Static variable in class etomica.util.Constants.Alignment
width - Variable in class org.jmol.util.GData
wigner3J(int, int, int, int, int, int) - Static method in class etomica.math.SpecialFunctions
Wigner3j - Class in etomica.veos.bigdecimal: Exact representations of Wigner 3jm and 3nj values of half-integer arguments.
Wigner3j() - Constructor for class etomica.veos.bigdecimal.Wigner3j
wigner3j(String, String, String, String) - Static method in class etomica.veos.bigdecimal.Wigner3j: Wigner 3jn symbol.
Wigner3jGUI - Class in etomica.veos.bigdecimal: An interactive interface to the Wigner3j class.
Wigner3jGUI() - Constructor for class etomica.veos.bigdecimal.Wigner3jGUI
wigner3jm(int, int, int, int, int, int) - Static method in class etomica.veos.bigdecimal.Wigner3j: The Wigner 3jm symbol (j1,j2,j3,m1,m2,m3).
wigner3jm(Rational, Rational, Rational, Rational, Rational, Rational) - Static method in class etomica.veos.bigdecimal.Wigner3j: The Wigner 3jm symbol (j1,j2,j3,m1,m2,m3).
wignerSeitzCell() - Method in class etomica.lattice.crystal.Primitive: Returns the Wigner-Seitz cell specified by this primitive.
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveBcc
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveCubic: Returns a new Square (if primitive is 2D) or Cube (if 3D) with edges given by the size of the primitive vectors.
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveFcc
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveGeneral
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
wignerSeitzCell() - Method in class etomica.models.hexane.PrimitiveHexane
willDiscardNextData() - Method in class etomica.util.HistoryCollapsingDiscard
willDiscardNextData() - Method in class etomica.util.HistoryComplete
willDiscardNextData() - Method in class etomica.util.HistoryScrolling
WINDOW_CLOSER - Static variable in class etomica.graphics.SimulationGraphic
windowcentered - Static variable in class org.jmol.script.Token
windowClosed(WindowEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
windowClosing(WindowEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
windowHeight - Variable in class org.jmol.util.GData
windowWidth - Variable in class org.jmol.util.GData
WIREFRAME - Static variable in class g3dsys.images.Bond
wireframe - Static variable in class org.jmol.script.Token
wireframerotation - Static variable in class org.jmol.script.Token
within - Static variable in class org.jmol.script.Token
withReplacement - Variable in class etomica.data.AccumulatorAverageCollapsingLog
wNew - Variable in class etomica.models.hexane.MCMoveCBMC
wNew - Variable in class etomica.virial.MCMoveClusterAngleBend
wNew - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
wNew - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
wNew - Variable in class etomica.virial.MCMoveClusterRingRegrow
wNew - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
wNew - Variable in class etomica.virial.MCMoveClusterRotateCH3
wNew - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
wNew - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
wNew - Variable in class etomica.virial.MCMoveClusterTorsionMulti
wNew - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
wNew - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
wNew - Variable in class etomica.virial.MCMoveClusterWiggleMulti
wOld - Variable in class etomica.models.hexane.MCMoveCBMC
wOld - Variable in class etomica.virial.MCMoveClusterAngleBend
wOld - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
wOld - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
wOld - Variable in class etomica.virial.MCMoveClusterRingRegrow
wOld - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
wOld - Variable in class etomica.virial.MCMoveClusterRotateCH3
wOld - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
wOld - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
wOld - Variable in class etomica.virial.MCMoveClusterTorsionMulti
wOld - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
wOld - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
wOld - Variable in class etomica.virial.MCMoveClusterWiggleMulti
work - Variable in class etomica.data.AccumulatorAverageBlockless
work - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
work - Variable in class etomica.data.AccumulatorAverageFixed
work - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
work - Variable in class etomica.data.DataSourceTensorVirialHard
work - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
work - Variable in class etomica.models.co2.PNCO2GCPM
work - Variable in class etomica.models.co2.PNGCPM
work - Variable in class etomica.models.nitrogen.P2Nitrogen
work - Variable in class etomica.models.nitrogen.P2NitrogenAB
work - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
work - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
work - Variable in class etomica.models.water.P2Water3P
work - Variable in class etomica.models.water.P2Water4P
work - Variable in class etomica.models.water.PNWaterGCPM
work - Variable in class etomica.modules.droplet.AtomFilterLiquid
work - Variable in class etomica.modules.rosmosis.P1Tether
work - Variable in class etomica.normalmode.MeterDDP
work - Variable in class etomica.normalmode.MeterDP
work - Variable in class etomica.potential.P2CO2EMP
work - Variable in class etomica.space3d.RotationTensor3D
work1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
work1 - Variable in class etomica.association.BiasVolumeAceticAcid
work1 - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
work1 - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
work1 - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
work1 - Variable in class etomica.virial.MCMoveClusterAngleBend
work1 - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
work1 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
work1 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
work1 - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
work1 - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
work1 - Variable in class etomica.virial.MCMoveClusterWiggleMulti
work2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
work2 - Variable in class etomica.association.BiasVolumeAceticAcid
work2 - Variable in class etomica.data.AccumulatorAverageFixed
work2 - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
work2 - Variable in class etomica.virial.MCMoveClusterAngleBend
work2 - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
work2 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
work2 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
work2 - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
work2 - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
work2 - Variable in class etomica.virial.MCMoveClusterWiggleMulti
work3 - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
work3 - Variable in class etomica.virial.MCMoveClusterAngleBend
work3 - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
work3 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
work3 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
work3 - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
work3 - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
work3 - Variable in class etomica.virial.MCMoveClusterWiggleMulti
workArray - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
workArray - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
workAveCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
workdTorq - Variable in class etomica.models.nitrogen.P2Nitrogen
workTensor - Variable in class etomica.integrator.IntegratorRigidIterative
workTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
workTensor - Variable in class etomica.integrator.IntegratorVelocityVerlet
workTensor - Variable in class etomica.integrator.IntegratorVerlet
workTensor - Variable in class etomica.models.water.OrientationCalcWater3P
workTensor - Variable in class etomica.models.water.OrientationCalcWater4P
workTensor - Variable in class etomica.modules.droplet.IntegratorDroplet
workTensor - Variable in class etomica.modules.droplet.MeterDeformation
workTensor - Variable in class etomica.potential.PotentialCalculationPressureTensor
workTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
workTensor2 - Variable in class etomica.modules.droplet.IntegratorDroplet
workTorqVec - Variable in class etomica.models.nitrogen.P2Nitrogen
workVec - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
workVec - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
workVec - Variable in class etomica.models.nitrogen.P2Nitrogen
workVector - Variable in class etomica.dimer.IntegratorDimerMin
workVector - Variable in class etomica.dimer.IntegratorDimerRT
workVector - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
workVector - Variable in class etomica.normalmode.CoordinateDefinitionLeaf
workVector - Variable in class etomica.normalmode.MeterAtomicDisplacement
workVector3 - Variable in class etomica.dimer.IntegratorDimerRT
wrappedCluster - Variable in class etomica.virial.ClusterCoupledFlipped
wrappedDataSource - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
wrappedPotential - Variable in class etomica.normalmode.P2XOrder
wrappedPotential - Variable in class etomica.potential.P2HardWrapper
wrappedPotential - Variable in class etomica.potential.P2MoleculeMonatomic
wrappedPotential - Variable in class etomica.potential.P2SoftTruncated
wrappedPotentialMaster - Variable in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
wrapper - Variable in class etomica.util.ParseArgs
wrapper - Variable in class etomica.util.ReadParameters
wrapper - Variable in class etomica.util.WriteParameters
wRatio - Variable in class etomica.virial.MCMoveClusterRingScale
write(Exception) - Method in interface etomica.graph.engine.Console
write(String) - Method in interface etomica.graph.engine.Console
write(Exception) - Method in class etomica.graph.engine.ConsoleUI
write(String) - Method in class etomica.graph.engine.ConsoleUI
write(Parser.CommandVariableValue) - Method in class etomica.graph.engine.Interpreter
writeAtom(FileWriter, IAtom) - Method in class etomica.action.WriteConfiguration
writeAtom(FileWriter, IAtom) - Method in class etomica.action.WriteConfigurationOriented
writeAtom(FileWriter, IAtom) - Method in class etomica.interfacial.WriteConfigurationInterfacial
WriteConfiguration - Class in etomica.action: Dumps a box's configuration to a file.
WriteConfiguration(ISpace) - Constructor for class etomica.action.WriteConfiguration
writeConfiguration(String) - Method in class etomica.kmc.IntegratorKMC
writeConfiguration(String) - Method in class etomica.kmc.IntegratorKMCCluster
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2TP
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
writeConfiguration(String) - Method in class etomica.normalmode.SimFluidSoftSphere
WriteConfigurationBinary - Class in etomica.action: Dumps a box's configuration to a file.
WriteConfigurationBinary(ISpace) - Constructor for class etomica.action.WriteConfigurationBinary
WriteConfigurationDLPOLY - Class in etomica.action: Dumps a box's configuration to a file.
WriteConfigurationDLPOLY() - Constructor for class etomica.action.WriteConfigurationDLPOLY
WriteConfigurationInterfacial - Class in etomica.interfacial: Dumps a box's configuration to a file.
WriteConfigurationInterfacial(ISpace) - Constructor for class etomica.interfacial.WriteConfigurationInterfacial
WriteConfigurationOriented - Class in etomica.action: WriteConfiguration subclass capable of handling oriented atoms.
WriteConfigurationOriented(ISpace) - Constructor for class etomica.action.WriteConfigurationOriented
WriteConfigurationP2DLPOLY - Class in etomica.action: Dumps a box's configuration to a file.
WriteConfigurationP2DLPOLY() - Constructor for class etomica.action.WriteConfigurationP2DLPOLY
writeD(AkimaSplineSmoother, String, int) - Static method in class etomica.util.numerical.AkimaSplineSmootherMain
writeData() - Method in interface etomica.threaded.IPotentialCalculationThreaded
writeData() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
writeData() - Method in class etomica.threads.ThreadsMD
writeData(String) - Method in class etomica.virial.MeterVirialBDBin
writeData(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
writeData(String, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
writeData(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
writeData(String, Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
writeData(String) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
writeData(String, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
writeDataToFile(String) - Method in class etomica.action.CalcVibrationalModes
writedb(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
writeDiagrams() - Method in class etomica.virial.cluster.ClusterDiagramTree
WriteHistograms - Class in etomica.models.oneDHardRods
WriteHistograms() - Constructor for class etomica.models.oneDHardRods.WriteHistograms
WriteHistograms(String) - Constructor for class etomica.models.oneDHardRods.WriteHistograms
writeLn() - Method in interface etomica.graph.engine.Console
writeLn() - Method in class etomica.graph.engine.ConsoleUI
writeMethod - Variable in class etomica.modifier.ModifierGeneral
WriteParameters - Class in etomica.util: This class writes input parameters from a parameter wrapper Object to a file.
WriteParameters() - Constructor for class etomica.util.WriteParameters
WriteParameters(String) - Constructor for class etomica.util.WriteParameters
WriteParameters(String, ParameterBase) - Constructor for class etomica.util.WriteParameters
writeParameters() - Method in class etomica.util.WriteParameters: Reads each line from inputFileName and attempts to match it with a field from parameterWrapper and sets the field to the value from the file.
writePosition - Variable in class etomica.action.WriteConfiguration
writePosition - Variable in class etomica.action.WriteConfigurationBinary
writer - Variable in class etomica.dimer.IntegratorDimerMin
writeRasmolScript(DiameterHashByType) - Method in class etomica.action.PDBWriter: Writes a script for rasmol that initializes the radii of each atom type.
writeRasmolScript(DiameterHashByType) - Method in class etomica.action.XYZWriter: Writes a script for rasmol that initializes the radii of each atom type.
writeRefPref - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
writeRefPref - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
writeRefPref - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
writeRefPref - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
writeRefPref - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
writeRefPref - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
WriteS - Class in etomica.normalmode: Class that writes out S from the MeterNormalMode, calculates eigenvectors/values (writes them out) and calculates the harmonic free energy from them.
WriteS(ISpace) - Constructor for class etomica.normalmode.WriteS
writeSetToFile(Set<Graph>, String) - Static method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
writeUdistribution(String) - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
writeUdistribution(String) - Method in class etomica.models.nitrogen.MeterOrientationDistribution
writeUdistribution(String) - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
writeWeights(String) - Method in class etomica.virial.MeterVirialBDBin
writeWeights(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
writeWeights(String, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
writeWeights(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
writeWeights(String, Map<IntSet, MeterVirialBinMultiThreaded.MyData>) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
writeWeights(String) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
writeWeights(String, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
wvCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
wvCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
wvTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic

X

X - Variable in class etomica.conjugategradient.ConjugateGradients
X - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
X - Variable in class etomica.conjugategradient.SteepestDescent
x - Variable in class etomica.data.types.DataDouble: The wrapped data value held by this object.
x - Variable in class etomica.data.types.DataTensor: The wrapped tensor data.
x - Variable in class etomica.data.types.DataVector: The wrapped vector data.
x - Variable in class etomica.nbr.CriterionPositionWall.DoubleWrapper
x - Variable in class etomica.space3d.Vector3D
x - Variable in class etomica.spaceNd.TensorND
x - Variable in class etomica.spaceNd.VectorND
x - Variable in class etomica.util.Grabber.CornerData
x - Variable in class etomica.util.numerical.AkimaSpline
x - Variable in class etomica.util.numerical.AkimaSplineSmoother
x - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
x - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
x - Variable in class etomica.util.numerical.NonLinearCurveFitting
x - Variable in class etomica.util.OdeSolver.Variables
x - Static variable in class org.jmol.script.Token
x - Variable in class org.jmol.util.AxisAngle4f: The x coordinate.
x - Variable in class org.jmol.util.Tuple3f: The x coordinate.
x - Variable in class org.jmol.util.Tuple3i: The x coordinate.
x - Variable in class org.jmol.util.Tuple4f: The x coordinate.
x0 - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
x0 - Variable in class etomica.mappedvirial.MappedUpotential
x0 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
x0 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
x0 - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
x0 - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
x0 - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
x0 - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
x0 - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
x1 - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
X_DIM - Static variable in class etomica.graphics.DevicePlotPoints
xCell - Variable in class etomica.normalmode.ModifierYCells2D
xd - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
xd - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
xData - Variable in class etomica.data.DataSourceRmsVelocity
xData - Variable in class etomica.mappedvirial.MeterMeanForce
xData - Variable in class etomica.modules.chainequilibrium.MeterChainLength
xData - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
xData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
xData - Variable in class etomica.normalmode.DataSourceFE
xData - Variable in class etomica.normalmode.DataSourceFEHistogram
xData - Variable in class etomica.normalmode.DataSourceImposedFEFit
xData - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
xData - Variable in class etomica.normalmode.DataSourcePMu
xData - Variable in class etomica.normalmode.DataSourcePN
xData - Variable in class etomica.normalmode.MeterTiltHistogram
xDataInfo - Variable in class etomica.data.DataSourceRmsVelocity
xDataInfo - Variable in class etomica.mappedvirial.MeterMeanForce
xDataInfo - Variable in class etomica.modules.chainequilibrium.MeterChainLength
xDataInfo - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
xDataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
xDataInfo - Variable in class etomica.normalmode.DataSourceFE
xDataInfo - Variable in class etomica.normalmode.DataSourceFEHistogram
xDataInfo - Variable in class etomica.normalmode.DataSourceImposedFEFit
xDataInfo - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
xDataInfo - Variable in class etomica.normalmode.DataSourcePMu
xDataInfo - Variable in class etomica.normalmode.DataSourcePN
xDataInfo - Variable in class etomica.normalmode.MeterTiltHistogram
xDataSource - Variable in class etomica.data.AccumulatorHistogram
xDataSource - Variable in class etomica.data.DataHistogram
xDataSource - Variable in class etomica.data.HistogramDataSource
xDataSource - Variable in class etomica.data.meter.MeterDihedralAngle
xDataSource - Variable in class etomica.data.meter.MeterProfileByAtoms
xDataSource - Variable in class etomica.data.meter.MeterProfileByVolume
xDataSource - Variable in class etomica.data.meter.MeterRDF
xDataSource - Variable in class etomica.data.meter.MeterRDFPC
xDataSource - Variable in class etomica.data.meter.PotentialCalculationRDF
xDataSource - Variable in class etomica.data.types.DataFunction.DataInfoFunction
xDataSource - Variable in class etomica.data.types.DataFunction.DataInfoFunctionFactory
xDataSource - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
xDataSource - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
xDataSource - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
xDataSource - Variable in class etomica.normalmode.MeterTiltRotationHistogram
xDataSource - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
xDataSource - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
xDataSources - Variable in class etomica.data.AccumulatorHistory
xDropAxis - Variable in class etomica.modules.droplet.DropletAtomic
XE(IVector) - Method in interface etomica.api.IVectorMutable: Sets this vector equal to the cross product of this vector with the given vector (only works for 3D vectors).
XE(IVector) - Method in class etomica.space1d.Vector1D
XE(IVector) - Method in class etomica.space2d.Vector2D
XE(IVector) - Method in class etomica.space3d.Vector3D
XE(IVector) - Method in class etomica.spaceNd.VectorND
xGT - Static variable in class org.jmol.util.GData
xicom - Variable in class etomica.util.numerical.Function1d
xIntercept() - Method in class etomica.math.geometry.Plane: Returns the intercept of the plane with the x-axis.
xLabel - Variable in class etomica.graphics.DisplayPlot
xLast - Variable in class org.jmol.util.GData
xLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
xlateDown() - Method in class g3dsys.control.G3DSys: Translate model 10% of pixel width down (+y)
xlateLeft() - Method in class g3dsys.control.G3DSys: Translate model 10% of pixel width to the left (-x)
xlateRight() - Method in class g3dsys.control.G3DSys: Translate model 10% of pixel width to the right (+x)
xlateUp() - Method in class g3dsys.control.G3DSys: Translate model 10% of pixel width up (-y)
xlateXY(int, int) - Method in class g3dsys.control.G3DSys: Trnaslate model x,y pixels
xLight - Static variable in class org.jmol.util.Shader
xlp - Static variable in class etomica.potential.P1HydrogenMielke
xLT - Static variable in class org.jmol.util.GData
xLxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
xMax - Variable in class etomica.data.meter.MeterRDF
xMax - Variable in class etomica.data.meter.MeterRDFPC
xMax - Variable in class etomica.data.meter.PotentialCalculationRDF
xMax - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
xMax - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
xMax - Variable in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
xMax - Variable in class etomica.util.HistogramNotSoSimple
xMax - Variable in class etomica.util.HistogramReweightedData
xMax - Variable in class etomica.util.HistogramSimple
xmax_ - Variable in class etomica.modules.clustergenerator.Plot
xMaxp - Variable in class etomica.potential.P3HydrogenManzhos
xMaxt - Variable in class etomica.potential.P3HydrogenManzhos
xMin - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
xMin - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
xMin - Variable in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
xMin - Variable in class etomica.util.HistogramNotSoSimple
xMin - Variable in class etomica.util.HistogramReweightedData
xMin - Variable in class etomica.util.HistogramSimple
xmin_ - Variable in class etomica.modules.clustergenerator.Plot
xMinp - Variable in class etomica.potential.P3HydrogenManzhos
xMint - Variable in class etomica.potential.P3HydrogenManzhos
xNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
xor(Bitmap) - Method in interface etomica.graph.model.Bitmap: Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap = (bitmap ^ other).
xor(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
xor(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong: TIME = O(1) for a compatible instance.
xor(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
xor(BitSet) - Method in class org.jmol.util.BitSet: Performs a logical XOR of this bit set with the bit set argument.
xPixel(double) - Method in class etomica.modules.clustergenerator.Plot: Computes the x pixel value of a point in the world window.
xPixels - Variable in class etomica.modules.clustergenerator.Plot
xPos - Static variable in class etomica.potential.P2HydrogenPatkowski
xPos - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
xPos - Variable in class etomica.potential.P3HydrogenManzhos
xSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
xTag - Variable in class etomica.data.DataSourceRmsVelocity
xTag - Variable in class etomica.mappedvirial.MeterMeanForce
xTag - Variable in class etomica.modules.chainequilibrium.MeterChainLength
xTag - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
xTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
xTag - Variable in class etomica.normalmode.DataSourceFE
xTag - Variable in class etomica.normalmode.DataSourceFEHistogram
xTag - Variable in class etomica.normalmode.DataSourceImposedFEFit
xTag - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
xTag - Variable in class etomica.normalmode.DataSourcePMu
xTag - Variable in class etomica.normalmode.DataSourcePN
xTag - Variable in class etomica.normalmode.MeterTiltHistogram
xTriplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
xType - Variable in class etomica.models.rowley.SpeciesEthanol
xType - Variable in class etomica.models.rowley.SpeciesMethanol
xValues() - Method in interface etomica.util.Histogram: Returns the x values from the histogram as an array of doubles
xValues - Variable in class etomica.util.HistogramDiscrete
xValues() - Method in class etomica.util.HistogramDiscrete
xValues - Variable in class etomica.util.HistogramNotSoSimple
xValues() - Method in class etomica.util.HistogramNotSoSimple
xValues - Variable in class etomica.util.HistogramReweightedData
xValues() - Method in class etomica.util.HistogramReweightedData
xValues - Variable in class etomica.util.HistogramSimple
xValues() - Method in class etomica.util.HistogramSimple
xValues - Variable in class etomica.util.HistoryCollapsing
xVecBox - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
xVecBox - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
xVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
xVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
xVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
xVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
xVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
xVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
xVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
xVecBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
xveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
xveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
xvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
xvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
xveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
xveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
xWork - Variable in class etomica.integrator.IntegratorRigidIterative
xWork - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
xWork - Variable in class etomica.models.water.OrientationCalcWater3P
xWork - Variable in class etomica.models.water.OrientationCalcWater4P
xWork - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
xx - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
xx - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
xx - Variable in class etomica.space3d.Tensor3D
xy - Variable in class etomica.space3d.Tensor3D
XY_ZTOP - Static variable in class org.jmol.viewer.JmolConstants
xyz - Static variable in class org.jmol.script.Token
XYZWriter - Class in etomica.action: Action that dumps a box's configuration to an XYZ file.
XYZWriter(IBox) - Constructor for class etomica.action.XYZWriter
xz - Variable in class etomica.space3d.Tensor3D
xz1 - Variable in class etomica.dimer.P1LepsHarmonic
xz2 - Variable in class etomica.dimer.P1LepsHarmonic
xzOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
xzOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
xzOrientationTensor - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular

Y

y - Variable in class etomica.data.meter.MeterProfileByAtoms
y - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
y - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
y - Variable in class etomica.potential.P3HydrogenManzhos
y - Variable in class etomica.space3d.Vector3D
y - Variable in class etomica.util.Grabber.CornerData
y - Variable in class etomica.util.numerical.AkimaSpline
y - Variable in class etomica.util.numerical.AkimaSplineSmoother
y - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
y - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
y - Variable in class etomica.util.numerical.NonLinearCurveDiffFitting
y - Variable in class etomica.util.numerical.NonLinearCurveFitting
Y - Variable in class etomica.util.numerical.PadeApproximation
y - Variable in class etomica.util.OdeSolver.Variables
y - Static variable in class org.jmol.script.Token
y - Variable in class org.jmol.util.AxisAngle4f: The y coordinate.
y - Variable in class org.jmol.util.Tuple3f: The y coordinate.
y - Variable in class org.jmol.util.Tuple3i: The y coordinate.
y - Variable in class org.jmol.util.Tuple4f: The y coordinate.
y0 - Variable in class etomica.util.numerical.AkimaSplineSmoother
y0 - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
y0 - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
Y_DIM - Static variable in class etomica.graphics.DevicePlotPoints
yCell - Variable in class etomica.normalmode.ModifierXCells2D
yDoublePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
YELLOW - Static variable in class org.jmol.util.Colix
YesRemoveSpeciesButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
yGT - Static variable in class org.jmol.util.GData
yIntercept() - Method in class etomica.math.geometry.Plane: Returns the intercept of the plane with the y-axis.
yLast - Variable in class org.jmol.util.GData
yLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
yLight - Static variable in class org.jmol.util.Shader
yLT - Static variable in class org.jmol.util.GData
yLxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
ymax_ - Variable in class etomica.modules.clustergenerator.Plot
ymin_ - Variable in class etomica.modules.clustergenerator.Plot
yNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
YOCTO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-24.
yOffset - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
yOffset - Variable in class etomica.modules.sam.ConfigurationSAM
yOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
yOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
yOrientationTensor - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
YOTTA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺²⁴.
yPixel(double) - Method in class etomica.modules.clustergenerator.Plot: Computes the y pixel value of a point in the world window.
yPixels - Variable in class etomica.modules.clustergenerator.Plot
ySmooth - Variable in class etomica.util.numerical.AkimaSplineSmootherApp
ySmooth - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
yTriplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
yTrue - Variable in class etomica.util.numerical.AkimaSplineSmootherDyApp
yVecBox - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
yVecBox - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
yVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
yVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
yVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
yVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
yVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
yVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
yVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
yVecBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
yveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
yveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
yvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
yvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
yveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
yveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
yWork - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
yWork - Variable in class etomica.models.water.OrientationCalcWater3P
yWork - Variable in class etomica.models.water.OrientationCalcWater4P
yx - Variable in class etomica.space3d.Tensor3D
yy - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
yy - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
yy - Variable in class etomica.space3d.Tensor3D
yz - Variable in class etomica.space3d.Tensor3D
yz1 - Variable in class etomica.dimer.P1LepsHarmonic
yz2 - Variable in class etomica.dimer.P1LepsHarmonic

Z

Z - Variable in class etomica.meam.ParameterSetMEAM
Z - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
z - Variable in class etomica.space3d.Vector3D
Z - Variable in class etomica.util.numerical.PadeApproximation
z - Static variable in class org.jmol.script.Token
z - Variable in class org.jmol.util.AxisAngle4f: The z coordinate.
z - Variable in class org.jmol.util.Tuple3f: The z coordinate.
z - Variable in class org.jmol.util.Tuple3i: The z coordinate.
z - Variable in class org.jmol.util.Tuple4f: The z coordinate.
Z3 - Variable in class etomica.potential.P3CPSNonAdditiveHe
Z3 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
Z3 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
Z3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
Z3_112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z3_113 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z3_122 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z3_222 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z4211 - Variable in class etomica.potential.P3CPSNonAdditiveHe
Z4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
Z4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
Z4211_1112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z4211_1121 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z4211_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z4220 - Variable in class etomica.potential.P3CPSNonAdditiveHe
Z4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
Z4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
Z4220_1111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z4220_1211 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
Z4220_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
zbuf - Variable in class org.jmol.g3d.Graphics3D
zbufT - Variable in class org.jmol.g3d.Graphics3D
zdepth - Static variable in class org.jmol.script.Token
zDepth - Variable in class org.jmol.util.GData
zDoublePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
Zeolite - Class in etomica.zeolite
Zeolite() - Constructor for class etomica.zeolite.Zeolite
zeoliteSimGraphic - Class in etomica.zeolite
zeoliteSimGraphic(ZeoliteSimulation, ISpace) - Constructor for class etomica.zeolite.zeoliteSimGraphic
zeoliteSimGraphic(ZeoliteSimulation, ISpace, String) - Constructor for class etomica.zeolite.zeoliteSimGraphic
ZeoliteSimStart - Class in etomica.zeolite
ZeoliteSimStart(ZeoliteSimulation, zeoliteSimGraphic) - Constructor for class etomica.zeolite.ZeoliteSimStart
ZeoliteSimStart(IntegratorMD, boolean, int) - Constructor for class etomica.zeolite.ZeoliteSimStart
ZeoliteSimulation - Class in etomica.zeolite: Three-dimensional hard-sphere molecular dynamics simulation, using neighbor listing.
ZEPTO - Static variable in class etomica.units.Prefix: Prefix indicating 10^-21.
ZERO - Static variable in class etomica.graph.model.BitmapFactory
ZERO - Static variable in class etomica.util.Rational
ZERO - Static variable in class etomica.veos.bigdecimal.BigSurd: The value of zero.
ZERO - Static variable in class etomica.veos.bigdecimal.BigSurdVec: The value of zero.
ZERO - Static variable in class etomica.veos.bigdecimal.Ifactor
ZERO - Static variable in class etomica.veos.bigdecimal.Rational: The constant 0.
ZERO - Static variable in class etomica.veos.BigValue
zerobasedxyzrasmol - Static variable in class org.jmol.script.Token
zeros - Static variable in class etomica.data.types.DataDoubleBDArray
zeroSum() - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff: Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
zeroSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
zeroSum() - Method in class etomica.potential.PotentialCalculationEnergySum: Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal: Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSum() - Method in class etomica.potential.PotentialCalculationHyperVirialSum: Sets the virial sum to zero, typically to begin a new virial-sum calculation.
zeroSum() - Method in class etomica.potential.PotentialCalculationMolecularVirialSum: Sets the virial sum to zero, typically to begin a new virial-sum calculation.
zeroSum() - Method in class etomica.potential.PotentialCalculationPhiSum
zeroSum() - Method in class etomica.potential.PotentialCalculationPressureTensor
zeroSum() - Method in class etomica.potential.PotentialCalculationVirialSum: Sets the virial sum to zero, typically to begin a new virial-sum calculation.
zeroSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff: Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeroSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoffLS: Sets the energy sum to zero, typically to begin a new energy-sum calculation.
zeta(int, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Riemann zeta function.
zeta1(int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath: Riemann zeta function.
ZETTA - Static variable in class etomica.units.Prefix: Prefix indicating 10⁺²¹.
ZFcc(double, double) - Static method in class etomica.statmech.LennardJones: Compressibility factor, P/rho/kT for the fcc solid.
zFluid(double) - Static method in class etomica.statmech.HardSphereFluid
zGT - Static variable in class org.jmol.util.GData
zIntercept() - Method in class etomica.math.geometry.Plane: Returns the intercept of the plane with the z-axis.
zk - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
zl - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
zLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
zLight - Static variable in class org.jmol.util.Shader
zLT - Static variable in class org.jmol.util.GData
zLxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
zMargin - Variable in class org.jmol.g3d.Graphics3D
zMax - Variable in class etomica.interfacial.ConfigurationLammps
zNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
zoomDown(int) - Method in class g3dsys.control.G3DSys: Decrease the zoom level by i percent
zoomenabled - Static variable in class org.jmol.script.Token
zoomlarge - Static variable in class org.jmol.script.Token
zoomUp(int) - Method in class g3dsys.control.G3DSys: Increase the zoom level by i percent
zQuadruplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
zshade - Static variable in class org.jmol.script.Token
zShadeB - Variable in class org.jmol.util.GData
zShadeG - Variable in class org.jmol.util.GData
zshadepower - Static variable in class org.jmol.script.Token
zShadePower - Variable in class org.jmol.util.GData
zShadeR - Variable in class org.jmol.util.GData
zShift - Variable in class etomica.interfacial.MeterWallPosition
zslab - Static variable in class org.jmol.script.Token
zSlab - Variable in class org.jmol.util.GData
zSolid(double) - Method in class etomica.statmech.HardSphere: Returns the compressibility factor for solid (FCC) hard spheres at the given density.
zSolid(double) - Static method in class etomica.statmech.HardSphereSolid: Returns the compressibility factor for solid (FCC) hard spheres at the given density.
zSolidCorrection(double) - Static method in class etomica.statmech.HardSphereSolid: Returns the correction to high density expression for the compressibility factor for solid (FCC) hard spheres at the given density.
zTriplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
zVecBox - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
zVecBox - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
zVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
zVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
zVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
zVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
zVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
zVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
zVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
zVecBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
zWork - Variable in class etomica.models.water.OrientationCalcWater3P
zWork - Variable in class etomica.models.water.OrientationCalcWater4P
zx - Variable in class etomica.space3d.Tensor3D
zy - Variable in class etomica.space3d.Tensor3D
zz - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
zz - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
zz - Variable in class etomica.space3d.Tensor3D

_

_3dEnabled - Static variable in class etomica.graphics.DisplayPolytope
_a - Variable in class g3dsys.images.Ellipse
_c - Variable in class g3dsys.images.Axes
_c - Variable in class g3dsys.images.Ball
_c - Variable in class g3dsys.images.Box
_c - Variable in class g3dsys.images.Ellipse
_c - Variable in class g3dsys.images.Line
_c - Variable in class g3dsys.images.Triangle
_d - Variable in class g3dsys.images.Ball
_d - Variable in class g3dsys.images.Bond
_d - Variable in class g3dsys.images.Ellipse
_gsys - Variable in class g3dsys.images.Figure
_id - Variable in class g3dsys.images.Figure
_p - Variable in class g3dsys.images.Ball
_p - Variable in class g3dsys.images.Ellipse

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _